# HG changeset patch
# User iuc
# Date 1521569814 14400
# Node ID 90c49ac0776e028a83d6a0f4bee2795db6a30342
# Parent  1f5904c5ee4238a48d2f0c933a91c2991049c332
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173

diff -r 1f5904c5ee42 -r 90c49ac0776e macros.xml
--- a/macros.xml	Wed Feb 14 10:11:07 2018 -0500
+++ b/macros.xml	Tue Mar 20 14:16:54 2018 -0400
@@ -124,8 +124,13 @@
     <xml name="param-printlevel">
         <param argument="printlevel" type="integer" value="-1" min="-1" label="Print level" help="specify taxlevel of your *tax.summary file to print to. Options are 1 to the maz level in the file. The default is -1, meaning max level" />
     </xml>
+    <xml name="param-savelog">
+        <param name="savelog" type="boolean" checked="false" label="Output logfile?"/>
+    </xml>
     <xml name="logfile-output">
-        <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/>
+        <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile">
+            <filter>savelog</filter>
+        </data>
     </xml>
 
     <!-- Output file tests -->
diff -r 1f5904c5ee42 -r 90c49ac0776e sub.sample.xml
--- a/sub.sample.xml	Wed Feb 14 10:11:07 2018 -0500
+++ b/sub.sample.xml	Tue Mar 20 14:16:54 2018 -0400
@@ -144,6 +144,7 @@
         <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/>
         <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
         <param name="taxonomy" type="data" format="mothur.seq.taxonomy,mothur.ref.taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -186,6 +187,7 @@
                    </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with list and group file and label select-->
@@ -203,6 +205,7 @@
                    </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with fasta and taxonomy -->
@@ -219,6 +222,7 @@
                     <has_line_matching expression="^U[0-9]+\tBacteria.*$"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with fasta and group file and name file -->
@@ -243,6 +247,7 @@
                     <has_line_matching expression="^U[0-9]+\tU[0-9]+$"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with shared -->
@@ -260,6 +265,7 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with rabund -->
@@ -271,6 +277,7 @@
                     <has_text text="0.55"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with sabund -->
@@ -282,6 +289,7 @@
                     <has_text text="0.55"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
diff -r 1f5904c5ee42 -r 90c49ac0776e tool_test_output_all.html
--- a/tool_test_output_all.html	Wed Feb 14 10:11:07 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,383 +0,0 @@
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-    <title>Tool Test Results (powered by Planemo)</title>
-
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-        var test_data = {"tests": [{"data": {"status": "success", "inputs": {"ss|source": "history", "fasta": {"src": "hda", "id": "2891970512fa2d5a"}, "ss|map": {"src": "hda", "id": "5729865256bc2525"}}, "job": {"inputs": {"map": {"src": "hda", "id": "5729865256bc2525", "uuid": "053e2ad0-e168-4120-ad32-52e2416a299a"}, "fasta": {"src": "hda", "id": "2891970512fa2d5a", "uuid": "0941ec90-8b06-453f-a07d-7377fcc259fa"}}, "update_time": "2018-02-08T16:48:16.346086", "tool_id": "mothur_align_check", "outputs": {"align.check": {"src": "hda", "id": "8155e4b4bf1581ff", "uuid": "6f898177-0cce-4858-827e-c5f55957a447"}, "logfile": {"src": "hda", "id": "54f2a3a23292eb07", "uuid": "8bcb8390-ff8f-49ef-920e-edc5eea5af5e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.check(fasta=fasta.dat,map=map.dat)\n\n\t\tPound\tDash\tPlus\tEqual\tLoop\tTilde\tTotal\nMinimum:\t0\t0\t0\t0\t0\t0\t0\n2.5%-tile:\t0\t0\t0\t0\t0\t0\t0\n25%-tile:\t0\t0\t0\t0\t0\t0\t0\nMedian: \t0\t0\t0\t0\t0\t0\t0\n75%-tile:\t0\t0\t0\t0\t0\t0\t0\n97.5%-tile:\t0\t0\t0\t0\t0\t0\t0\nMaximum:\t0\t0\t0\t0\t0\t0\t0\n# of Seqs:\t3\n\nOutput File Names: \nfasta.align.check\n\n\nmothur > quit\nname\tpound\tdash\tplus\tequal\tloop\ttilde\ttotal\tnumseqs\nU68589\t0\t0\t0\t0\t0\t0\t0\t1\nU68590\t0\t0\t0\t0\t0\t0\t0\t1\nU68591\t0\t0\t0\t0\t0\t0\t0\t1\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_1.dat' fasta.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_2.dat' map.dat &&  echo 'align.check( fasta=fasta.dat, map=map.dat )' | sed 's/ //g' | mothur | tee mothur.out.log && cat fasta.align.check", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:48:13.244725", "params": {"count": "null", "ss": "{\"source\": \"history\", \"__current_case__\": 1, \"map\": {\"values\": [{\"src\": \"hda\", \"id\": 2}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6024", "id": "54f2a3a23292eb07", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_check.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"ss|source": "history", "fasta": {"src": "hda", "id": "7b55dbb89df8f4e5"}, "name": {"src": "hda", "id": "683bc220e21425bb"}, "ss|map": {"src": "hda", "id": "fa6d20d0fb68383f"}}, "job": {"inputs": {"map": {"src": "hda", "id": "fa6d20d0fb68383f", "uuid": "097857e5-ed1d-4947-bce3-6fd2905a34d3"}, "fasta": {"src": "hda", "id": "7b55dbb89df8f4e5", "uuid": "bd1c7e31-c02d-42a6-aadc-13ca52654e33"}, "name": {"src": "hda", "id": "683bc220e21425bb", "uuid": "2e360511-c984-432e-85d3-1f609059f22b"}}, "update_time": "2018-02-08T16:48:40.077690", "tool_id": "mothur_align_check", "outputs": {"align.check": {"src": "hda", "id": "b842d972534ccb3e", "uuid": "a01d16ed-d559-4e00-b362-4037248e1858"}, "logfile": {"src": "hda", "id": "a90a30fafe298e1e", "uuid": "e866176f-3e93-4d33-b079-6bba2ce39eda"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.check(fasta=fasta.dat,name=name.dat,map=map.dat)\n\n\t\tPound\tDash\tPlus\tEqual\tLoop\tTilde\tTotal\nMinimum:\t0\t0\t0\t0\t0\t0\t0\n2.5%-tile:\t0\t0\t0\t0\t0\t0\t0\n25%-tile:\t0\t0\t0\t0\t0\t0\t0\nMedian: \t0\t0\t0\t0\t0\t0\t0\n75%-tile:\t0\t0\t0\t0\t0\t0\t0\n97.5%-tile:\t0\t0\t0\t0\t0\t0\t0\nMaximum:\t0\t0\t0\t0\t0\t0\t0\n# of unique seqs:\t3\ntotal # of seqs:\t3\n\nOutput File Names: \nfasta.align.check\n\n\nmothur > quit\nname\tpound\tdash\tplus\tequal\tloop\ttilde\ttotal\tnumseqs\nU68589\t0\t0\t0\t0\t0\t0\t0\t1\nU68590\t0\t0\t0\t0\t0\t0\t0\t1\nU68591\t0\t0\t0\t0\t0\t0\t0\t1\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_5.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_7.dat' name.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_6.dat' map.dat &&  echo 'align.check( fasta=fasta.dat, name=name.dat, map=map.dat )' | sed 's/ //g' | mothur | tee mothur.out.log && cat fasta.align.check", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:48:36.966637", "params": {"count": "null", "ss": "{\"source\": \"history\", \"__current_case__\": 1, \"map\": {\"values\": [{\"src\": \"hda\", \"id\": 6}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6167", "id": "683bc220e21425bb", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_check.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "5449172d6ff5669b"}, "alignment|reference": {"src": "hda", "id": "9ce08b2254e4d5ed"}, "alignment|source": "history"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "5449172d6ff5669b", "uuid": "1511b135-9600-43ec-91ca-20164079249a"}, "reference": {"src": "hda", "id": "9ce08b2254e4d5ed", "uuid": "2ef10dca-7831-4e85-bab7-f42bbd443a69"}}, "update_time": "2018-02-08T16:49:00.881405", "tool_id": "mothur_align_seqs", "outputs": {"report": {"src": "hda", "id": "1ae74d26531588b0", "uuid": "5aec6e8b-0ee3-4a6f-aa99-cc598c48e677"}, "logfile": {"src": "hda", "id": "80b8022ff3f677b7", "uuid": "b8c8daf3-d155-49f0-8e41-c3be034495a8"}, "out_align": {"src": "hda", "id": "b54fb481e575bccc", "uuid": "50a15fa3-f47b-446b-b906-ca3c5b1d1d79"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=need \rleman,ksize=8,processors=1)\n\nUsing 1 processors.\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read  32 sequences.\nAligning sequences from fasta.dat ...\n22\nIt took 0 secs to align 22 sequences.\n\n\nOutput File Names: \nfasta.align\nfasta.align.report\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s `dirname $(which mothur)`/* . &&  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_10.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_11.dat' alignment.reference.dat &&  echo 'align.seqs( fasta=fasta.dat, reference=alignment.reference.dat, align=needleman, ksize=8, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | ./mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:48:57.586073", "params": {"scoring": "{\"adjust\": \"no\", \"__current_case__\": 1}", "search": "{\"method\": \"kmer\", \"__current_case__\": 0, \"ksize\": \"8\"}", "reverse": "{\"flip\": \"no\", \"__current_case__\": 1}", "align": "\"needleman\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"history\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 11}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6286", "id": "5449172d6ff5669b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"scoring|adjust": "yes", "alignment|reference": {"src": "hda", "id": "ea0b941dfbe636f8"}, "search|method": "kmer", "alignment|source": "history", "scoring|gapopen": "-6", "scoring|mismatch": "-15", "scoring|match": "2", "fasta": {"src": "hda", "id": "440a6c2b5d9efe20"}, "scoring|gapextend": "-3"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "440a6c2b5d9efe20", "uuid": "3057b911-5600-4c3c-b9f6-35b7b93693e9"}, "reference": {"src": "hda", "id": "ea0b941dfbe636f8", "uuid": "1ed348d0-821e-41d1-ac7a-4318df4ccfb4"}}, "update_time": "2018-02-08T16:49:26.757457", "tool_id": "mothur_align_seqs", "outputs": {"report": {"src": "hda", "id": "d5b3e51b7b790121", "uuid": "6d8c3d0a-b428-4f86-ae91-09e4e56c859f"}, "logfile": {"src": "hda", "id": "27ee89e2e3d631e0", "uuid": "f47ef7f7-8a17-466f-8150-4a3aa88cab8d"}, "out_align": {"src": "hda", "id": "61f03d5eef6f1538", "uuid": "5c082a64-10a1-41aa-815a-75e92ba5145a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=need \rleman,ksize=8,match=2,mismatch=-15,gapopen=-6,gapextend=-3,processors=1)\n\nUsing 1 processors.\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read  32 sequences.\nAligning sequences from fasta.dat ...\n22\nIt took 0 secs to align 22 sequences.\n\n\nOutput File Names: \nfasta.align\nfasta.align.report\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s `dirname $(which mothur)`/* . &&  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_15.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_16.dat' alignment.reference.dat &&  echo 'align.seqs( fasta=fasta.dat, reference=alignment.reference.dat, align=needleman, ksize=8, match=2, mismatch=-15, gapopen=-6, gapextend=-3, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | ./mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:49:23.290890", "params": {"scoring": "{\"gapopen\": \"-6\", \"mismatch\": \"-15\", \"adjust\": \"yes\", \"__current_case__\": 0, \"gapextend\": \"-3\", \"match\": \"2\"}", "search": "{\"method\": \"kmer\", \"__current_case__\": 0, \"ksize\": \"8\"}", "reverse": "{\"flip\": \"no\", \"__current_case__\": 1}", "align": "\"needleman\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"history\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 16}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6412", "id": "b54fb481e575bccc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"scoring|adjust": "yes", "alignment|reference": {"src": "hda", "id": "c18708cec3343c17"}, "search|method": "suffix", "align": "gotoh", "alignment|source": "history", "scoring|gapopen": "-6", "scoring|mismatch": "-15", "scoring|match": "2", "fasta": {"src": "hda", "id": "b28067233c6d9fa0"}, "scoring|gapextend": "-3"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "b28067233c6d9fa0", "uuid": "a898f88c-9854-45b4-b978-8f6e8c19a035"}, "reference": {"src": "hda", "id": "c18708cec3343c17", "uuid": "69a4e7a8-77db-46bd-8b24-a45f4df43f0b"}}, "update_time": "2018-02-08T16:49:55.216327", "tool_id": "mothur_align_seqs", "outputs": {"report": {"src": "hda", "id": "a1e670e1ea0da54b", "uuid": "302f7300-55b1-4314-9556-7004d1c9fe2c"}, "logfile": {"src": "hda", "id": "5ca39fba41b940d1", "uuid": "ec2c6d47-b9a7-4d62-b5b9-7bf44a852e2c"}, "out_align": {"src": "hda", "id": "3e4e8de146a035f5", "uuid": "edca646b-7964-4384-8097-96d24e09046f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=goto \rh,search=suffix,match=2,mismatch=-15,gapopen=-6,gapextend=-3,processors=1)\n\nUsing 1 processors.\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read  32 sequences.\nAligning sequences from fasta.dat ...\n22\nIt took 0 secs to align 22 sequences.\n\n\nOutput File Names: \nfasta.align\nfasta.align.report\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s `dirname $(which mothur)`/* . &&  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_20.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_21.dat' alignment.reference.dat &&  echo 'align.seqs( fasta=fasta.dat, reference=alignment.reference.dat, align=gotoh, search=suffix, match=2, mismatch=-15, gapopen=-6, gapextend=-3, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | ./mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:49:51.967514", "params": {"scoring": "{\"gapopen\": \"-6\", \"mismatch\": \"-15\", \"adjust\": \"yes\", \"__current_case__\": 0, \"gapextend\": \"-3\", \"match\": \"2\"}", "search": "{\"method\": \"suffix\", \"__current_case__\": 1}", "reverse": "{\"flip\": \"no\", \"__current_case__\": 1}", "align": "\"gotoh\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"history\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 21}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6539", "id": "ea0b941dfbe636f8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"reverse|threshold": "0.5", "reverse|flip": "yes", "search|method": "blast", "alignment|source": "history", "alignment|reference": {"src": "hda", "id": "0535d515f68130b3"}, "fasta": {"src": "hda", "id": "9a22496ee796fbfc"}, "align": "blast"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "9a22496ee796fbfc", "uuid": "bf930a57-cb72-465c-9544-d8fab031b1b9"}, "reference": {"src": "hda", "id": "0535d515f68130b3", "uuid": "82704b74-e2ca-4ce7-adec-4995d8f13f83"}}, "update_time": "2018-02-08T16:50:21.251688", "tool_id": "mothur_align_seqs", "outputs": {"report": {"src": "hda", "id": "073082a17e1b2f0b", "uuid": "6df7f08f-1df2-4678-9895-34a65f4be0a8"}, "flip_accnos": {"src": "hda", "id": "a908e285532ac9b0", "uuid": "8d49424e-a5ed-4167-bd8f-f1306b9ffebd"}, "logfile": {"src": "hda", "id": "238993350abc9bfd", "uuid": "6d52e61a-30c4-4bf8-bb2a-25d0aac7dcbc"}, "out_align": {"src": "hda", "id": "adba32ec9811aba7", "uuid": "d8f8e608-698b-471f-b7cb-777a2e7a7e53"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=blas \rt,search=blast,flip=true,threshold=0.5,processors=1)\n\nUsing 1 processors.\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read  32 sequences.\nAligning sequences from fasta.dat ...\n22\nIt took 0 secs to align 22 sequences.\n\n\nOutput File Names: \nfasta.align\nfasta.align.report\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s `dirname $(which mothur)`/* . &&  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_25.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_26.dat' alignment.reference.dat &&  echo 'align.seqs( fasta=fasta.dat, reference=alignment.reference.dat, align=blast, search=blast, flip=true, threshold=0.5, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | ./mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:50:17.543144", "params": {"scoring": "{\"adjust\": \"no\", \"__current_case__\": 1}", "search": "{\"method\": \"blast\", \"__current_case__\": 2}", "reverse": "{\"threshold\": \"0.5\", \"flip\": \"yes\", \"__current_case__\": 0}", "align": "\"blast\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"history\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 26}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6655", "id": "d5b3e51b7b790121", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment|source": "history", "reverse|threshold": "0.5", "reverse|flip": "yes", "fasta": {"src": "hda", "id": "27a22803849b1486"}, "alignment|reference": {"src": "hda", "id": "3777da040b354424"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "27a22803849b1486", "uuid": "6f889445-9480-4dfe-99a4-640d4d6f292f"}, "reference": {"src": "hda", "id": "3777da040b354424", "uuid": "0d421449-2afb-4639-aa7d-92fe9f605482"}}, "update_time": "2018-02-08T16:50:51.061674", "tool_id": "mothur_align_seqs", "outputs": {"report": {"src": "hda", "id": "05f80801815deda8", "uuid": "0c8e178c-f0da-4eb3-9766-01c4c2d3416a"}, "flip_accnos": {"src": "hda", "id": "95a5ac7e4618a243", "uuid": "ff4586a2-2f5c-4ae4-9d13-3b32eccfe2b7"}, "logfile": {"src": "hda", "id": "2d785e48ad6d0148", "uuid": "676f6060-0b7f-41c4-be36-5774428ebebc"}, "out_align": {"src": "hda", "id": "840f77504195704d", "uuid": "6e22fcea-953a-4218-930d-853351145ba8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=need \rleman,ksize=8,flip=true,threshold=0.5,processors=1)\n\nUsing 1 processors.\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read  32 sequences.\nAligning sequences from fasta.dat ...\n98\n[WARNING]: Some of your sequences generated alignments that eliminated too many bases, a list is provided in fasta.flip.accnos. If the reverse compliment proved to be better it was reported.\nIt took 1 secs to align 98 sequences.\n\n\nOutput File Names: \nfasta.align\nfasta.align.report\nfasta.flip.accnos\n\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s `dirname $(which mothur)`/* . &&  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_31.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_32.dat' alignment.reference.dat &&  echo 'align.seqs( fasta=fasta.dat, reference=alignment.reference.dat, align=needleman, ksize=8, flip=true, threshold=0.5, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | ./mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:50:47.166993", "params": {"scoring": "{\"adjust\": \"no\", \"__current_case__\": 1}", "search": "{\"method\": \"kmer\", \"__current_case__\": 0, \"ksize\": \"8\"}", "reverse": "{\"threshold\": \"0.5\", \"flip\": \"yes\", \"__current_case__\": 0}", "align": "\"needleman\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"history\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 32}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6892", "id": "5ca39fba41b940d1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_align_seqs.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"phylip": {"src": "hda", "id": "863b4912f43ba501"}, "design": {"src": "hda", "id": "a068cbb083194156"}}, "job": {"inputs": {"phylip": {"src": "hda", "id": "863b4912f43ba501", "uuid": "bd47e735-1d66-48e8-85b2-5cb23c5910da"}, "design": {"src": "hda", "id": "a068cbb083194156", "uuid": "b297c9ec-d075-46b6-a8b9-0a26269db239"}}, "update_time": "2018-02-08T16:51:24.191000", "tool_id": "mothur_amova", "outputs": {"logfile": {"src": "hda", "id": "bb70618268111ce1", "uuid": "ae1be271-e920-4241-82dc-c9c3086c860d"}, "amova": {"src": "hda", "id": "f16a54a3ef316466", "uuid": "8ee19962-9e76-40a7-8c8e-595fdc6b675a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > amova(phylip=phylip.dat,iters=1000,alpha=0.05,design=design.dat)\nA-B\tAmong\tWithin\tTotal\nSS\t0.04869\t4.72878\t4.77747\ndf\t1\t96\t97\nMS\t0.04869\t0.0492581\n\nFs:\t0.988466\np-value: 0.458\n\nExperiment-wise error rate: 0.05\nIf you have borderline P-values, you should try increasing the number of iterations\n\nOutput File Names: \nphylip.amova\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_37.dat' phylip.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_38.dat' design.dat &&  echo 'amova( phylip=phylip.dat, iters=1000, alpha=0.05, design=design.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:51:20.982934", "params": {"iters": "\"1000\"", "alpha": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "sets": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7011", "id": "9a22496ee796fbfc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_amova.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"phylip": {"src": "hda", "id": "e511a12dc2cf12e1"}, "design": {"src": "hda", "id": "25f486d5fc93a1ce"}}, "job": {"inputs": {"phylip": {"src": "hda", "id": "e511a12dc2cf12e1", "uuid": "d9fa0ca2-ecc1-4a59-a245-4aa165e1ddd8"}, "design": {"src": "hda", "id": "25f486d5fc93a1ce", "uuid": "d8d23a72-a2c6-4587-8694-92d2d5d9694a"}}, "update_time": "2018-02-08T16:51:45.688705", "tool_id": "mothur_anosim", "outputs": {"logfile": {"src": "hda", "id": "244c246e3628fe4f", "uuid": "fd4ccc15-8aca-438d-a74b-13c4e3d53183"}, "anosim": {"src": "hda", "id": "8c9b639396181d1e", "uuid": "3fc29196-23fd-4ee4-a1cd-e44881657963"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > anosim(phylip=phylip.dat,iters=1000,alpha=0.05,design=design.dat)\n\ncomparison\tR-value\tP-value\nA-B\t-0.00786503\t0.803\n\nExperiment-wise error rate: 0.05\nIf you have borderline P-values, you should try increasing the number of iterations\n\nOutput File Names: \nphylip.anosim\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_41.dat' phylip.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_42.dat' design.dat &&  echo 'anosim( phylip=phylip.dat, iters=1000, alpha=0.05, design=design.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:51:42.659886", "params": {"iters": "\"1000\"", "alpha": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7171", "id": "adba32ec9811aba7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_anosim.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "3f322b493a2c6407"}, "otu": {"src": "hda", "id": "616a01dfb111aa65"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "3f322b493a2c6407", "uuid": "a4414c4a-10ad-49a7-898b-ea5e812efe13"}, "otu": {"src": "hda", "id": "616a01dfb111aa65", "uuid": "7434bb32-62f4-4bf8-9c54-e7dd572a2c96"}}, "update_time": "2018-02-08T16:52:08.320737", "tool_id": "mothur_bin_seqs", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "48f3e8809447c25a", "uuid": "82255b24-0f88-412b-ac83-4169df892ddb"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "bcb334d054d0b7ff", "uuid": "07f9a0b2-3558-490b-a4be-3666561874d5"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "087a78e08fef416e", "uuid": "c09649da-75d2-42fb-87eb-f84b3d976439"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "a6b9cabbe61f73ca", "uuid": "b3af742b-d000-4a66-b58b-40ba1aa441e6"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "288a67f7f32bb2fd", "uuid": "05d8f777-6439-45d3-8728-8bb62ce73dd5"}, "__new_primary_file_unique|0.16__": {"src": "hda", "id": "9649d2d367737693", "uuid": "b7db14ef-f926-478c-9efc-c902c834a38f"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "945d4aa2c8920004", "uuid": "e7446bee-fbb5-41fc-ad27-5022478132c7"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "bab99c776d4b9391", "uuid": "514147bf-71da-4aa2-9cf5-749b73813977"}, "__new_primary_file_unique|0.15__": {"src": "hda", "id": "9268a0f969417b28", "uuid": "4af76395-320c-4f71-897d-101bcbe66a89"}, "__new_primary_file_unique|0.08__": {"src": "hda", "id": "0e797101c95aea67", "uuid": "ae90e95f-c5d9-40a9-bb67-808f3781b410"}, "__new_primary_file_unique|0.14__": {"src": "hda", "id": "4ec7f8db939dbc03", "uuid": "41e9763e-8502-4f82-987c-6bcadeac8c99"}, "__new_primary_file_unique|0.13__": {"src": "hda", "id": "b908d9d86f8a3d36", "uuid": "85c4005f-926f-45f4-aed6-5a1761fdc78d"}, "__new_primary_file_unique|0.09__": {"src": "hda", "id": "baa1080356b320b7", "uuid": "1d245aaa-593e-4858-bb72-99a06bd16a2b"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "f8cc3c3467afd773", "uuid": "ef61051b-92ef-4e4f-8072-f73c13337b44"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "03229f6bce6358e8", "uuid": "034876ff-b15d-4736-b637-e0b2651498ce"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "85f590476b78f8ed", "uuid": "6dddc8da-c256-41c4-8e09-5e54a864ce97"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "315992a54eac5ecc", "uuid": "46af4cfc-722a-4cfb-9e82-4b7b21b4d650"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "5e6ad6ca0afeaf24", "uuid": "f997f7fc-426f-4878-a3da-82263f0d56cf"}, "__new_primary_file_unique|0.25__": {"src": "hda", "id": "ca4ebafec84c6506", "uuid": "443e82af-ee52-4570-aba4-6f6c70b2cf24"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "fed9b1622ba4118e", "uuid": "e9e9f881-f8fb-4895-ba58-3a6d576e9652"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "a94ebc130565c5b1", "uuid": "d7181b5c-5b42-4dc7-95e2-90aa2c31a4b0"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "dccb60510b24da2f", "uuid": "44a715ff-3bbe-42fb-aefa-bc39b6edb766"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "b323ca264f40001e", "uuid": "55b4447a-958d-4da0-8729-16c09d97e464"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "0ed16744ccfa2592", "uuid": "a9523881-2f20-46a2-8562-6286e628bea3"}, "logfile": {"src": "hda", "id": "25cc0305829779de", "uuid": "7d161dc7-876c-4537-9422-0f6dbbcce3b2"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "5617b66919498d02", "uuid": "7eca21fd-952c-48e9-b065-ad8faf6890f7"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "4163d05c3cc243fc", "uuid": "601b3468-2d3a-42fb-94ec-5ec4d44c5ba0"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "c57c922a3f91222f", "uuid": "210756e0-0676-4ffe-9552-6254ac608881"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "f276a8cc85beb7f0", "uuid": "e8840d4f-f1b7-4d78-ad58-d78d06ab1a97"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "0ff3854aee1a95dd", "uuid": "0e733526-2d9b-47ce-8226-86822da0cfed"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "b31f4d82ada5e956", "uuid": "efe00c7e-df09-4162-a39e-7e3ad6b6992b"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "87dca8aa4ee9d3de", "uuid": "6523651c-1ec4-4bd0-b61c-43cff9a14b35"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "a96f5ebdac2d8d75", "uuid": "276db109-89f3-4bc8-95bb-f5ed726886fc"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "fb9b740929ea3f54", "uuid": "8f1f88dd-1218-4481-922a-a4d0407edc75"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "1c6e228e19b11e1b", "uuid": "79e53fa2-5eca-41cb-94b5-6294a1de4784"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "08fbf3fbfe908f7c", "uuid": "afa5db0d-aef3-48f8-8272-f62179616e19"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "2987a55ca6380b3a", "uuid": "9ed42128-8ed0-4fb0-8899-f3675ff10a2c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > bin.seqs(fasta=fasta.dat,list=otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.fasta\notu.0.01.fasta\notu.0.02.fasta\notu.0.03.fasta\notu.0.04.fasta\notu.0.05.fasta\notu.0.06.fasta\notu.0.07.fasta\notu.0.08.fasta\notu.0.09.fasta\notu.0.10.fasta\notu.0.11.fasta\notu.0.12.fasta\notu.0.13.fasta\notu.0.14.fasta\notu.0.15.fasta\notu.0.16.fasta\notu.0.17.fasta\notu.0.18.fasta\notu.0.19.fasta\notu.0.20.fasta\notu.0.21.fasta\notu.0.22.fasta\notu.0.23.fasta\notu.0.24.fasta\notu.0.25.fasta\notu.0.26.fasta\notu.0.27.fasta\notu.0.29.fasta\notu.0.32.fasta\notu.0.33.fasta\notu.0.36.fasta\notu.0.38.fasta\notu.0.41.fasta\notu.0.45.fasta\notu.0.55.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s 'None' name.dat && ln -s 'None' group.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_45.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_46.dat' otu.dat && ln -s 'None' count.dat &&  echo 'bin.seqs( fasta=fasta.dat, list=otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:52:03.131907", "params": {"count": "null", "group": "null", "name": "null", "dbkey": "\"hg17\"", "label": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7287", "id": "27a22803849b1486", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_bin_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "f1e243926043ec87"}, "label": ["0.03", "0.05", "0.22"], "group": {"src": "hda", "id": "19ec6936a7590160"}, "otu": {"src": "hda", "id": "73de4610aed2490c"}, "name": {"src": "hda", "id": "df545be7ad5cd764"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "f1e243926043ec87", "uuid": "c435f069-2cb4-401d-b4b6-f13dc04e0f48"}, "group": {"src": "hda", "id": "19ec6936a7590160", "uuid": "d4862a29-d42f-4c4c-8200-bb560e04e0fc"}, "name": {"src": "hda", "id": "df545be7ad5cd764", "uuid": "cf3ab84b-8a5c-46d0-b016-c567300ff9bd"}, "otu": {"src": "hda", "id": "73de4610aed2490c", "uuid": "630b9f6c-7e41-453f-a3a1-1e61ce6cbf73"}}, "update_time": "2018-02-08T16:52:37.247581", "tool_id": "mothur_bin_seqs", "outputs": {"__new_primary_file_0.22|0.22__": {"src": "hda", "id": "97f8596e58df898c", "uuid": "76baa1ae-3604-4d9c-b169-ccc567946ec3"}, "logfile": {"src": "hda", "id": "330fe5822b24a25f", "uuid": "5acd7d94-805c-4499-a898-0b4846b38603"}, "__new_primary_file_0.22|0.05__": {"src": "hda", "id": "adcc13f516c5d573", "uuid": "d5c89c69-11b2-4bc4-a480-785f8f546e38"}, "__new_primary_file_0.22|0.03__": {"src": "hda", "id": "3d556e8e35b754dc", "uuid": "1fe58d24-effc-454d-b5f8-aec9adaed90d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > bin.seqs(name=name.dat,group=group.dat,label=0.03-0.05-0.22,fasta=fasta \r.dat,list=otu.dat)\n0.03\n0.05\n0.22\n\nOutput File Names: \notu.0.03.fasta\notu.0.05.fasta\notu.0.22.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_86.dat' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_87.dat' group.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_84.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_85.dat' otu.dat && ln -s 'None' count.dat &&  echo 'bin.seqs( name=name.dat, group=group.dat, label=0.03-0.05-0.22, fasta=fasta.dat, list=otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:52:34.180038", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.22\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7458", "id": "95a5ac7e4618a243", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_bin_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"biom": {"src": "hda", "id": "e5cd870596a22f3d"}}, "job": {"inputs": {"biom": {"src": "hda", "id": "e5cd870596a22f3d", "uuid": "67321c4f-07f3-4496-a259-7d117cea03f2"}}, "update_time": "2018-02-08T16:52:54.726633", "tool_id": "mothur_biom_info", "outputs": {"shared": {"src": "hda", "id": "8e7a170d28bd3e46", "uuid": "4f910a6e-fda9-42b8-a952-3a560dba90af"}, "logfile": {"src": "hda", "id": "4923f2d7e29ffb4f", "uuid": "8176bc7a-5017-4c4b-9111-1e9c7ffb0df8"}, "tax.summary": {"src": "hda", "id": "facf9cd8e60ad8cf", "uuid": "97fe1137-5c9b-460b-8428-ac899fa45989"}, "taxonomy": {"src": "hda", "id": "2fd653ff8fe916b4", "uuid": "827a2b58-7246-42d2-b94f-3b732d61fefb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > biom.info(biom=input.biom,label=userLabel,basis=otu,output=simple,relab \rund=F,printlevel=-1)\n\nuserLabel\n\nIt took 0 create mothur files from your biom file.\n\n\nOutput File Names: \ninput.userLabel.shared\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_92.dat' input.biom &&  echo 'biom.info( biom=input.biom, label=userLabel, basis=otu, output=simple, relabund=F, printlevel=-1 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:52:51.473940", "params": {"relabund": "\"false\"", "basis": "\"otu\"", "dbkey": "\"hg17\"", "label": "\"userLabel\"", "printlevel": "\"-1\"", "output": "\"simple\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7557", "id": "a068cbb083194156", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_biom_info.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"biom": {"src": "hda", "id": "27a98c5f1b1968ef"}}, "job": {"inputs": {"biom": {"src": "hda", "id": "27a98c5f1b1968ef", "uuid": "b908b050-c74b-4347-9782-3755018efab3"}}, "update_time": "2018-02-08T16:53:12.209875", "tool_id": "mothur_biom_info", "outputs": {"shared": {"src": "hda", "id": "c0ae89d2a79fffb2", "uuid": "f4472a81-c659-4978-8fd9-e91063d57521"}, "logfile": {"src": "hda", "id": "4f5573cc87ed03c8", "uuid": "49be22ce-821c-47e7-9b1a-0a27db8b435f"}, "tax.summary": {"src": "hda", "id": "b028110e32789f9f", "uuid": "29e87425-3e47-45a2-82d6-ec9b97531e8d"}, "taxonomy": {"src": "hda", "id": "7e4191b982566cec", "uuid": "01441a21-25e1-4649-a372-5bc7e9f9732f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > biom.info(biom=input.biom,label=userLabel,basis=otu,output=simple,relab \rund=F,printlevel=-1)\n\nuserLabel\n\nIt took 0 create mothur files from your biom file.\n\n\nOutput File Names: \ninput.userLabel.shared\ninput.userLabel.cons.taxonomy\ninput.userLabel.cons.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_97.dat' input.biom &&  echo 'biom.info( biom=input.biom, label=userLabel, basis=otu, output=simple, relabund=F, printlevel=-1 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:53:09.050031", "params": {"relabund": "\"false\"", "basis": "\"otu\"", "dbkey": "\"hg17\"", "label": "\"userLabel\"", "printlevel": "\"-1\"", "output": "\"simple\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7642", "id": "f16a54a3ef316466", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_biom_info.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"basis": "sequence", "output": "detail", "printlevel": "4", "label": "0.03", "biom": {"src": "hda", "id": "2aec3223e9c2f754"}}, "job": {"inputs": {"biom": {"src": "hda", "id": "2aec3223e9c2f754", "uuid": "ceb35272-ae07-460b-9c0f-c4287106f26d"}}, "update_time": "2018-02-08T16:53:39.840477", "tool_id": "mothur_biom_info", "outputs": {"shared": {"src": "hda", "id": "0a3452e55f15c193", "uuid": "88445107-8ce0-4cdf-9706-fbaa9b955b00"}, "logfile": {"src": "hda", "id": "20de7af3d288c35f", "uuid": "2c3d7d5f-12eb-4fe3-96f6-aed61451fdbd"}, "tax.summary": {"src": "hda", "id": "bd73887c155f3ede", "uuid": "b29a8bcb-c556-4272-8253-f2be5dcca19d"}, "taxonomy": {"src": "hda", "id": "7f39b8b663207ef1", "uuid": "6b18fa32-dd9f-4bcb-9063-7deafdd5c733"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > biom.info(biom=input.biom,label=0.03,basis=sequence,output=detail,relab \rund=F,printlevel=4)\n\n0.03\n\nIt took 0 create mothur files from your biom file.\n\n\nOutput File Names: \ninput.0.03.shared\ninput.0.03.cons.taxonomy\ninput.0.03.cons.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_102.dat' input.biom &&  echo 'biom.info( biom=input.biom, label=0.03, basis=sequence, output=detail, relabund=F, printlevel=4 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:53:36.530476", "params": {"relabund": "\"false\"", "basis": "\"sequence\"", "dbkey": "\"hg17\"", "label": "\"0.03\"", "printlevel": "\"4\"", "output": "\"detail\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7734", "id": "25f486d5fc93a1ce", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_biom_info.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "69ce05044577833e"}, "window": "-1"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "69ce05044577833e", "uuid": "4a4ca0f1-a747-4892-9e90-04b34813c88f"}}, "update_time": "2018-02-08T16:54:07.782597", "tool_id": "mothur_chimera_bellerophon", "outputs": {"bellerophon.chimeras": {"src": "hda", "id": "3654d500199ce491", "uuid": "b675145d-c6c4-42df-a6e9-e4f20f2707e6"}, "logfile": {"src": "hda", "id": "4942bca139ae755c", "uuid": "b79f6a27-827d-490c-bd89-c79da2102d71"}, "bellerophon.accnos": {"src": "hda", "id": "a46b181036e98e92", "uuid": "ebae94f6-1fe2-4c17-baa8-2a033cd00057"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.bellerophon(fasta=fasta.dat,filter=False,correction=True,increm \rent=25,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nReading sequences from fasta.dat...Done.\nProcessing sliding window: 5\nM00967_43_000000000-A3JHG_1_1101_10073_7632 is a suspected chimera at breakpoint 88\nIt's score is 1.6254 with suspected left parent M00967_43_000000000-A3JHG_1_1101_8480_7498 and right parent M00967_43_000000000-A3JHG_1_1101_8480_7498\nM00967_43_000000000-A3JHG_1_1101_8480_7498 is a suspected chimera at breakpoint 88\nIt's score is 1.6254 with suspected left parent M00967_43_000000000-A3JHG_1_1101_10073_7632 and right parent M00967_43_000000000-A3JHG_1_1101_10073_7632\nM00967_43_000000000-A3JHG_1_1101_23552_5194 is a suspected chimera at breakpoint 138\nIt's score is 1.16994 with suspected left parent M00967_43_000000000-A3JHG_1_1101_7079_6722 and right parent M00967_43_000000000-A3JHG_1_1101_7079_6722\nM00967_43_000000000-A3JHG_1_1101_5170_7771 is a suspected chimera at breakpoint 138\nIt's score is 1.11972 with suspected left parent M00967_43_000000000-A3JHG_1_1101_13293_4703 and right parent M00967_43_000000000-A3JHG_1_1101_13293_4703\nM00967_43_000000000-A3JHG_1_1101_13293_4703 is a suspected chimera at breakpoint 138\nIt's score is 1.11972 with suspected left parent M00967_43_000000000-A3JHG_1_1101_11148_6457 and right parent M00967_43_000000000-A3JHG_1_1101_11148_6457\nM00967_43_000000000-A3JHG_1_1101_11148_6457 is a suspected chimera at breakpoint 138\nIt's score is 1.11972 with suspected left parent M00967_43_000000000-A3JHG_1_1101_13293_4703 and right parent M00967_43_000000000-A3JHG_1_1101_13293_4703\nM00967_43_000000000-A3JHG_1_1101_24357_4866 is a suspected chimera at breakpoint 138\nIt's score is 1.02604 with suspected left parent M00967_43_000000000-A3JHG_1_1101_11790_7581 and right parent M00967_43_000000000-A3JHG_1_1101_11790_7581\nM00967_43_000000000-A3JHG_1_1101_11790_7581 is a suspected chimera at breakpoint 138\nIt's score is 1.02604 with suspected left parent M00967_43_000000000-A3JHG_1_1101_24357_4866 and right parent M00967_43_000000000-A3JHG_1_1101_24357_4866\nM00967_43_000000000-A3JHG_1_1101_15923_3823 is a suspected chimera at breakpoint 138\nIt's score is 1.0226 with suspected left parent M00967_43_000000000-A3JHG_1_1101_7326_5417 and right parent M00967_43_000000000-A3JHG_1_1101_7326_5417\nM00967_43_000000000-A3JHG_1_1101_7326_5417 is a suspected chimera at breakpoint 138\nIt's score is 1.0226 with suspected left parent M00967_43_000000000-A3JHG_1_1101_15923_3823 and right parent M00967_43_000000000-A3JHG_1_1101_15923_3823\nM00967_43_000000000-A3JHG_1_1101_15208_7185 is a suspected chimera at breakpoint 138\nIt's score is 1.0226 with suspected left parent M00967_43_000000000-A3JHG_1_1101_15923_3823 and right parent M00967_43_000000000-A3JHG_1_1101_15923_3823\nM00967_43_000000000-A3JHG_1_1101_7079_6722 is a suspected chimera at breakpoint 138\nIt's score is 1.01583 with suspected left parent M00967_43_000000000-A3JHG_1_1101_23552_5194 and right parent M00967_43_000000000-A3JHG_1_1101_23552_5194\n\nSequence with preference score above 1.0: 12\nMinimum:\t0.682701\n2.5%-tile:\t0.682701\n25%-tile:\t0.837302\nMedian: \t1.01583\n75%-tile:\t1.11972\n97.5%-tile:\t1.6254\nMaximum:\t1.6254\n\nIt took 0 secs to check 22 sequences.\n\n\nOutput File Names: \nfasta.bellerophon.chimeras\nfasta.bellerophon.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_107.dat' fasta.dat &&  echo 'chimera.bellerophon( fasta=fasta.dat, filter=False, correction=True, increment=25, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:54:04.495851", "params": {"correction": "\"true\"", "dbkey": "\"hg17\"", "filter": "\"false\"", "window": "\"-1\"", "increment": "\"25\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7832", "id": "8c9b639396181d1e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_bellerophon.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "00c35829965cb81b"}, "alignment|reference": {"src": "hda", "id": "566489874e32c504"}, "alignment|source": "hist"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "00c35829965cb81b", "uuid": "67503ee2-ad54-4780-bde6-14f9662c2d6d"}, "reference": {"src": "hda", "id": "566489874e32c504", "uuid": "fe96ace6-a92a-47c6-b67d-573970b930d0"}}, "update_time": "2018-02-08T16:54:39.839013", "tool_id": "mothur_chimera_ccode", "outputs": {"ccode.chimeras": {"src": "hda", "id": "1fb9c7b21f94ef77", "uuid": "bc86b0c8-6d13-47d9-a386-f39638719b24"}, "logfile": {"src": "hda", "id": "e7d42a199e1d2420", "uuid": "b942c08b-5e97-4757-bb2c-3a4a440024ff"}, "ccode.accnos": {"src": "hda", "id": "c299b389e85e4513", "uuid": "4c11cc11-c934-41ef-887e-f3590ea4f715"}, "mapinfo": {"src": "hda", "id": "cf18f77993464b22", "uuid": "be0c8b32-7ab5-4dca-985b-17129a55606c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.ccode(fasta=fasta.dat,reference=alignment.template.dat,filter=F \ralse,numwanted=20,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nReading sequences from alignment.template.dat...Done.\nM00967_43_000000000-A3JHG_1_1101_7326_5417 was found have at least one chimeric window.\nProcessing sequence: 10\n\nIt took 1 secs to check 10 sequences.\n\nOutput File Names: \nfasta.ccode.chimeras\nfasta.mapinfo\nfasta.ccode.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_111.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_112.dat' alignment.template.dat &&  echo 'chimera.ccode( fasta=fasta.dat, reference=alignment.template.dat, filter=False, numwanted=20, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:54:35.274166", "params": {"numwanted": "\"20\"", "dbkey": "\"hg17\"", "filter": "\"false\"", "window": "\"0\"", "mask_cond": "{\"source2\": \"\", \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 112}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7952", "id": "25cc0305829779de", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_ccode.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "7ea23f5e4ed72fcd"}, "alignment|reference": {"src": "hda", "id": "161ef5576377f4a0"}, "window": "100", "alignment|source": "hist", "mask_cond|source2": "default"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "7ea23f5e4ed72fcd", "uuid": "a7f568a1-096d-4715-a052-f419660e59b2"}, "reference": {"src": "hda", "id": "161ef5576377f4a0", "uuid": "871b1483-4128-403f-b26a-080be516b889"}}, "update_time": "2018-02-08T16:55:13.593399", "tool_id": "mothur_chimera_ccode", "outputs": {"ccode.chimeras": {"src": "hda", "id": "f21e60058e4146e2", "uuid": "9e3f3299-f941-4c90-854e-f0c9c1e461e6"}, "logfile": {"src": "hda", "id": "ba60dc8fe2d987d5", "uuid": "d2c0e7c6-bcc6-4632-a668-37944112eef9"}, "ccode.accnos": {"src": "hda", "id": "4826aef2afaebe4b", "uuid": "5b78ccd6-a9c6-4fff-b063-175f0412a1e5"}, "mapinfo": {"src": "hda", "id": "c95281174db2641a", "uuid": "92ac37ff-50a5-4ad1-b132-a261727351bf"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.ccode(fasta=fasta.dat,reference=alignment.template.dat,filter=F \ralse,mask=default,window=100,numwanted=20,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nI am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013.\nReading sequences from alignment.template.dat...Done.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_19936_3208 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity.  I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_19936_3208 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_15923_3823 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_14010_4122 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity.  I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_14010_4122 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_13293_4703 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity.  I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_13293_4703 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_24357_4866 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_23552_5194 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity.  I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_23552_5194 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_7326_5417 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_11148_6457 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity.  I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_11148_6457 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_7079_6722 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity.  I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_7079_6722 was found have at least one chimeric window.\nYou have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.M00967_43_000000000-A3JHG_1_1101_8607_6805 does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity.  I will continue, but please check.\nM00967_43_000000000-A3JHG_1_1101_8607_6805 was found have at least one chimeric window.\nProcessing sequence: 10\n\nIt took 1 secs to check 10 sequences.\n\nOutput File Names: \nfasta.default.ccode.chimeras\nfasta.mapinfo\nfasta.default.ccode.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_117.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_118.dat' alignment.template.dat &&  echo 'chimera.ccode( fasta=fasta.dat, reference=alignment.template.dat, filter=False, mask=default, window=100, numwanted=20, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:55:09.142586", "params": {"numwanted": "\"20\"", "dbkey": "\"hg17\"", "filter": "\"false\"", "window": "\"100\"", "mask_cond": "{\"source2\": \"default\", \"__current_case__\": 2}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 118}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8064", "id": "bab99c776d4b9391", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_ccode.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "bd8ef6624a47d26f"}, "alignment|reference": {"src": "hda", "id": "39209c3a4b0cef4c"}, "alignment|source": "hist"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "bd8ef6624a47d26f", "uuid": "afb976b9-ef60-4b12-a931-c027c8cef9a2"}, "reference": {"src": "hda", "id": "39209c3a4b0cef4c", "uuid": "9e147cf5-6480-4227-b024-e04e1e4ef7e2"}}, "update_time": "2018-02-08T16:55:49.157744", "tool_id": "mothur_chimera_check", "outputs": {"logfile": {"src": "hda", "id": "26b7e36460fca86e", "uuid": "a2a768ac-9391-4632-9810-2d0d9c806298"}, "chimeracheck.chimeras": {"src": "hda", "id": "eb21622d9b6e26b4", "uuid": "d6031a8a-cb57-41e2-98e2-ed5829d4972d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.check(fasta=fasta.dat,reference=alignment.reference.dat,increme \rnt=10,ksize=7,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read  32 sequences.\n\nProcessing: M00967_43_000000000-A3JHG_1_1101_19936_3208\nProcessing: M00967_43_000000000-A3JHG_1_1101_15923_3823\nProcessing: M00967_43_000000000-A3JHG_1_1101_14010_4122\nProcessing: M00967_43_000000000-A3JHG_1_1101_13293_4703\nProcessing: M00967_43_000000000-A3JHG_1_1101_24357_4866\nProcessing: M00967_43_000000000-A3JHG_1_1101_23552_5194\nProcessing: M00967_43_000000000-A3JHG_1_1101_7326_5417\nProcessing: M00967_43_000000000-A3JHG_1_1101_11148_6457\nProcessing: M00967_43_000000000-A3JHG_1_1101_7079_6722\nProcessing: M00967_43_000000000-A3JHG_1_1101_8607_6805\nProcessing sequence: 10\n\nThis method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values.\n\nIt took 3 secs to check 10 sequences.\n\n\nOutput File Names: \nfasta.chimeracheck.chimeras\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_123.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_124.dat' alignment.reference.dat &&  echo 'chimera.check( fasta=fasta.dat, reference=alignment.reference.dat, increment=10, ksize=7, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:55:43.089163", "params": {"svg_cond": "{\"svg\": \"no\", \"__current_case__\": 0}", "dbkey": "\"hg17\"", "ksize": "\"7\"", "increment": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 124}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8186", "id": "5e6ad6ca0afeaf24", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_check.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "598efe8f302ea8ae"}, "svg_cond|name": {"src": "hda", "id": "e9cf7d8d4867436b"}, "svg_cond|svg": "yes", "alignment|source": "hist", "alignment|reference": {"src": "hda", "id": "5c14fa19c3fe9aa2"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "598efe8f302ea8ae", "uuid": "9ddbdf54-67b8-4edd-a6e9-bb7604e31dc4"}, "name": {"src": "hda", "id": "e9cf7d8d4867436b", "uuid": "75ab04f2-b35c-467b-88d1-a899fa003606"}, "reference": {"src": "hda", "id": "5c14fa19c3fe9aa2", "uuid": "9a079bc8-ceb1-4c5e-82df-a59c14e77494"}}, "update_time": "2018-02-08T16:56:16.969800", "tool_id": "mothur_chimera_check", "outputs": {"logfile": {"src": "hda", "id": "fc5c2ad70cbb4f9f", "uuid": "ac4cefa6-bfaa-4401-be90-336ca98d7b8f"}, "__new_primary_file_M00967_43_000000000-A3JHG_1_1101_14010_4122|M00967_43_000000000-A3JHG_1_1101_14010_4122__": {"src": "hda", "id": "83e248eabb1b3d31", "uuid": "9000d45e-4973-4578-99f2-617d128cb499"}, "chimeracheck.chimeras": {"src": "hda", "id": "5e985d59d5900484", "uuid": "e280ac0c-fac1-4b3c-a13d-b7885916062b"}, "__new_primary_file_M00967_43_000000000-A3JHG_1_1101_14010_4122|M00967_43_000000000-A3JHG_1_1101_13293_4703__": {"src": "hda", "id": "2f2abd7e16b39826", "uuid": "bbdec5e0-e4dc-448a-9007-43d0b3a0f8d0"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.check(fasta=fasta.dat,reference=alignment.reference.dat,svg=yes \r,name=svg.name.dat,increment=10,ksize=7,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\n\nReading in the alignment.reference.dat template sequences...\tDONE.\nIt took 0 to read  32 sequences.\n\nProcessing: M00967_43_000000000-A3JHG_1_1101_19936_3208\nProcessing: M00967_43_000000000-A3JHG_1_1101_15923_3823\nProcessing: M00967_43_000000000-A3JHG_1_1101_14010_4122\nProcessing: M00967_43_000000000-A3JHG_1_1101_13293_4703\nProcessing: M00967_43_000000000-A3JHG_1_1101_24357_4866\nProcessing: M00967_43_000000000-A3JHG_1_1101_23552_5194\nProcessing: M00967_43_000000000-A3JHG_1_1101_7326_5417\nProcessing: M00967_43_000000000-A3JHG_1_1101_11148_6457\nProcessing: M00967_43_000000000-A3JHG_1_1101_7079_6722\nProcessing: M00967_43_000000000-A3JHG_1_1101_8607_6805\nProcessing sequence: 10\n\nThis method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values.\n\nIt took 3 secs to check 10 sequences.\n\n\nOutput File Names: \nfasta.chimeracheck.chimeras\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_127.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_128.dat' alignment.reference.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_129.dat' svg.name.dat &&  echo 'chimera.check( fasta=fasta.dat, reference=alignment.reference.dat, svg=yes, name=svg.name.dat, increment=10, ksize=7, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:56:10.148586", "params": {"svg_cond": "{\"svg\": \"yes\", \"name\": {\"values\": [{\"src\": \"hda\", \"id\": 129}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\"", "ksize": "\"7\"", "increment": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 128}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8324", "id": "48f3e8809447c25a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_check.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "a01e20e32f0965d9"}, "name": {"src": "hda", "id": "4e27b888e0f89616"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "a01e20e32f0965d9", "uuid": "8521e069-b6cd-4c45-b6e5-8f7e69e73bba"}, "name": {"src": "hda", "id": "4e27b888e0f89616", "uuid": "491e5558-aa9e-46c8-846f-1bbb96a90abb"}}, "update_time": "2018-02-08T16:56:43.817915", "tool_id": "mothur_chimera_perseus", "outputs": {"out_chimeras": {"src": "hda", "id": "d760e1d92679b730", "uuid": "b722e5b1-053c-44cf-a2f8-7286ea3d18e4"}, "logfile": {"src": "hda", "id": "15839f6e830b1abe", "uuid": "420f680c-4cb1-4cdf-8752-30f636784f1e"}, "out_accnos": {"src": "hda", "id": "237cecdf0f984d5b", "uuid": "ea9ffc98-afb0-4985-86d3-80850d6525a1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.perseus(fasta=fasta.dat,name=name.dat,alpha=-5.54,beta=0.33,cut \roff=0.5,dereplicate=false,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nProcessing sequence: 98\n\nIt took 0 secs to check 98 sequences. 0 chimeras were found.\n\nOutput File Names: \nfasta.perseus.chimeras\nfasta.perseus.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_134.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_135.dat' name.dat && ln -s 'None' group.dat &&  echo 'chimera.perseus( fasta=fasta.dat, name=name.dat, alpha=-5.54, beta=0.33, cutoff=0.5, dereplicate=false, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:56:40.622188", "params": {"dereplicate": "\"false\"", "group": "null", "cutoff": "\"0.5\"", "dbkey": "\"hg17\"", "beta": "\"0.33\"", "alpha": "\"-5.54\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8441", "id": "b908d9d86f8a3d36", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_perseus.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment|source": "hist", "quantile": {"src": "hda", "id": "449eb427f528cea7"}, "window": "200", "fasta": {"src": "hda", "id": "3995f2aeb4b1e9b8"}, "alignment|reference": {"src": "hda", "id": "43c20e86f8351b08"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "3995f2aeb4b1e9b8", "uuid": "1b6d12bd-53eb-4adf-a8c9-2d517a1a06c2"}, "quantile": {"src": "hda", "id": "449eb427f528cea7", "uuid": "0dac3ed3-c5b1-4c88-a6cd-a09f73785ecb"}, "reference": {"src": "hda", "id": "43c20e86f8351b08", "uuid": "88a5d249-7780-4cc3-905d-5a78e67947c0"}}, "update_time": "2018-02-08T16:57:10.496322", "tool_id": "mothur_chimera_pintail", "outputs": {"out_freq": {"src": "hda", "id": "8bfda5654e551614", "uuid": "ea730516-89b4-498e-ba79-cba6bea15f91"}, "logfile": {"src": "hda", "id": "05698cd4bb850c59", "uuid": "2f32594b-954f-4c6e-bb7f-10246c03305d"}, "out_accnos": {"src": "hda", "id": "4674f339b90935da", "uuid": "bbe2d533-8860-40b9-8ce5-7fe8ea944655"}, "pintail.chimeras": {"src": "hda", "id": "bfa55a0374b9a6bf", "uuid": "d9543da6-6d05-4a3f-9017-9b3eb6fa0d4f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.pintail(fasta=fasta.dat,reference=alignment.reference.dat,filte \rr=false,quantile=quantile.dat,window=200,increment=25,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nReading sequences from alignment.reference.dat...Done.\nGetting conservation... Calculating probability of conservation for your template sequences.  This can take a while...  I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command.  Providing the .freq file will improve speed.    Done.\n\nM00967_43_000000000-A3JHG_1_1101_15923_3823\tdiv: 26.9841\tstDev: 1.41584\tchimera flag: Yes\nM00967_43_000000000-A3JHG_1_1101_13293_4703\tdiv: 29.3651\tstDev: 1.59916\tchimera flag: Yes\nM00967_43_000000000-A3JHG_1_1101_24357_4866\tdiv: 26.5873\tstDev: 1.39697\tchimera flag: Yes\nM00967_43_000000000-A3JHG_1_1101_11148_6457\tdiv: 29.3651\tstDev: 1.59916\tchimera flag: Yes\nProcessing sequence: 10\n\n\nIt took 2 secs to check 10 sequences.\n\nOutput File Names: \nfasta.pintail.chimeras\nfasta.pintail.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_139.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_140.dat' alignment.reference.dat && ln -s 'None' conservation.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_141.dat' quantile.dat &&  echo 'chimera.pintail( fasta=fasta.dat, reference=alignment.reference.dat, filter=false, quantile=quantile.dat, window=200, increment=25, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:57:04.307339", "params": {"increment": "\"25\"", "dbkey": "\"hg17\"", "filter": "\"false\"", "window": "\"200\"", "conservation": "null", "mask_cond": "{\"source2\": \"\", \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 140}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8577", "id": "087a78e08fef416e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_pintail.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "7959e4ab20d6a14d"}, "alignment|reference": {"src": "hda", "id": "54ea706d2daa88f1"}, "window": "200", "alignment|source": "hist", "mask_cond|source2": "default"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "7959e4ab20d6a14d", "uuid": "6839dbc1-616a-4882-96ea-ce6b374044f0"}, "reference": {"src": "hda", "id": "54ea706d2daa88f1", "uuid": "a32c495f-3e9b-4732-8ec6-129955955c3b"}}, "update_time": "2018-02-08T16:57:38.924061", "tool_id": "mothur_chimera_pintail", "outputs": {"out_freq": {"src": "hda", "id": "2567f547ea0518b1", "uuid": "d49dd2af-548c-4371-838d-2da9e7ca1379"}, "logfile": {"src": "hda", "id": "0b8510c6952c9474", "uuid": "e114c580-5d03-48e9-81c5-8cdccff4565a"}, "out_accnos": {"src": "hda", "id": "db1aec3269b07642", "uuid": "07a38fd5-d854-4740-bf6b-281d87ca512b"}, "pintail.chimeras": {"src": "hda", "id": "c48fc7b200585e1b", "uuid": "457f3666-d072-481c-a032-41dc8ed38044"}, "out_quantile": {"src": "hda", "id": "ac2ea1acb48016aa", "uuid": "eb5bca93-0ccf-4b62-a247-6ddd34b86c46"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.pintail(fasta=fasta.dat,reference=alignment.reference.dat,filte \rr=false,mask=default,window=200,increment=25,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nI am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013.\nReading sequences from alignment.reference.dat...Done.\nGetting conservation... Calculating probability of conservation for your template sequences.  This can take a while...  I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command.  Providing the .freq file will improve speed.    Done.\n\nCalculating quantiles for your template.  This can take a while...  I will output the quantiles to a .quan file that you can input them using the quantiles parameter next time you run this command.  Providing the .quan file will dramatically improve speed.    Processing sequence 0\nProcessing sequence 1\nYou have selected too large a window size for sequence A.odontolyticus.1.  I will choose an appropriate window size.\nProcessing sequence 2\nYou have selected too large a window size for sequence B.cereus.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.cereus.1.  I will choose an appropriate window size.\nProcessing sequence 3\nYou have selected too large a window size for sequence B.vulgatus.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.1.  I will choose an appropriate window size.\nProcessing sequence 4\nYou have selected too large a window size for sequence B.vulgatus.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.2.  I will choose an appropriate window size.\nProcessing sequence 5\nYou have selected too large a window size for sequence B.vulgatus.4.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.4.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.4.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.4.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.4.  I will choose an appropriate window size.\nProcessing sequence 6\nYou have selected too large a window size for sequence B.vulgatus.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.5.  I will choose an appropriate window size.\nProcessing sequence 7\nYou have selected too large a window size for sequence B.vulgatus.7.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.7.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.7.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.7.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.7.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.7.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence B.vulgatus.7.  I will choose an appropriate window size.\nProcessing sequence 8\nYou have selected too large a window size for sequence C.beijerinckii.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.1.  I will choose an appropriate window size.\nProcessing sequence 9\nYou have selected too large a window size for sequence C.beijerinckii.3.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.3.  I will choose an appropriate window size.\nProcessing sequence 10\nYou have selected too large a window size for sequence C.beijerinckii.4.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence C.beijerinckii.4.  I will choose an appropriate window size.\nProcessing sequence 11\nYou have selected too large a window size for sequence D.radiodurans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence D.radiodurans.1.  I will choose an appropriate window size.\nProcessing sequence 12\nYou have selected too large a window size for sequence E.faecalis.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.1.  I will choose an appropriate window size.\nProcessing sequence 13\nYou have selected too large a window size for sequence E.faecalis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.faecalis.2.  I will choose an appropriate window size.\nProcessing sequence 14\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence E.coli.1.  I will choose an appropriate window size.\nProcessing sequence 15\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence H.pylori.1.  I will choose an appropriate window size.\nProcessing sequence 16\nYou have selected too large a window size for sequence L.gasseri.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence L.gasseri.1.  I will choose an appropriate window size.\nYou have selected too large a window size f\n..\nte window size.\nYou have selected too large a window size for sequence S.epidermidis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.2.  I will choose an appropriate window size.\nProcessing sequence 28\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.epidermidis.5.  I will choose an appropriate window size.\nProcessing sequence 29\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.agalactiae.1.  I will choose an appropriate window size.\nProcessing sequence 30\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.mutans.1.  I will choose an appropriate window size.\nProcessing sequence 31\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence S.pneumoniae.1.  I will choose an appropriate window size.\nDone.\nReading sequences from alignment.reference.dat...Done.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_19936_3208.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_15923_3823.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_14010_4122.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_13293_4703.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_24357_4866.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_23552_5194.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_7326_5417.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_11148_6457.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_7079_6722.  I will choose an appropriate window size.\nYou have selected too large a window size for sequence M00967_43_000000000-A3JHG_1_1101_8607_6805.  I will choose an appropriate window size.\nProcessing sequence: 10\n\n\nIt took 3 secs to check 10 sequences.\n\nOutput File Names: \nfasta.default.pintail.chimeras\nfasta.default.pintail.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_146.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_147.dat' alignment.reference.dat && ln -s 'None' conservation.dat && ln -s 'None' quantile.dat &&  echo 'chimera.pintail( fasta=fasta.dat, reference=alignment.reference.dat, filter=false, mask=default, window=200, increment=25, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:57:32.943369", "params": {"increment": "\"25\"", "quantile": "null", "dbkey": "\"hg17\"", "filter": "\"false\"", "window": "\"200\"", "conservation": "null", "mask_cond": "{\"source2\": \"default\", \"__current_case__\": 2}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 147}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8698", "id": "5617b66919498d02", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_pintail.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "3af8c7b9f683116f"}, "alignment|reference": {"src": "hda", "id": "d7d0eb8e9bed0c39"}, "alignment|source": "hist"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "3af8c7b9f683116f", "uuid": "0c3c0bcd-0458-4195-af6b-c079b4996632"}, "reference": {"src": "hda", "id": "d7d0eb8e9bed0c39", "uuid": "96ffc55e-61f9-4e01-b8b1-5d270f2f9d1a"}}, "update_time": "2018-02-08T16:58:10.044025", "tool_id": "mothur_chimera_slayer", "outputs": {"slayer.chimeras": {"src": "hda", "id": "3f47e446edb5d442", "uuid": "f920d4ae-4e8c-4f4e-b1c9-386711a26402"}, "logfile": {"src": "hda", "id": "b7d4a98a7bb9e1bc", "uuid": "ba043b24-a39a-41e6-bffc-0e07740ed585"}, "out_accnos": {"src": "hda", "id": "8984b162f62c6c24", "uuid": "19589feb-b856-43dd-a3ee-1441b657ddea"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.slayer(fasta=fasta.dat,reference=/tmp/saskia/tmpKSDp0p/files/00 \r0/dataset_154.dat,dereplicate=false,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nReading sequences from /tmp/saskia/tmpKSDp0p/files/000/dataset_154.dat...Done.\n\nOnly reporting sequence supported by 90% of bootstrapped results.\nProcessing sequence: 10\nIt took 0 secs to check 10 sequences.\n\nOutput File Names: \nfasta.slayer.chimeras\nfasta.slayer.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s ln -s `dirname $(which mothur)`/* . &&  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_153.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_154.dat' alignment.reference.dat &&  echo 'chimera.slayer( fasta=fasta.dat, reference=/tmp/saskia/tmpKSDp0p/files/000/dataset_154.dat, dereplicate=false, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | ./mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:58:06.756216", "params": {"dereplicate": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 154}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\"", "options": "{\"setby\": \"default\", \"__current_case__\": 0}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8814", "id": "b323ca264f40001e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_slayer.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"options|setby": "user", "fasta": {"src": "hda", "id": "50c648a3603e917e"}, "options|search": "kmer", "alignment|source": "self", "alignment|name": {"src": "hda", "id": "71db30c33f7a1d97"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "50c648a3603e917e", "uuid": "b5946a78-cf06-49cd-baed-908c4ba5a099"}, "name": {"src": "hda", "id": "71db30c33f7a1d97", "uuid": "e5af7032-d15c-490d-8f99-315bab985aaa"}}, "update_time": "2018-02-08T16:58:30.636077", "tool_id": "mothur_chimera_slayer", "outputs": {"slayer.chimeras": {"src": "hda", "id": "c6239e5379f31f0f", "uuid": "bbdfd559-4c07-4742-adbe-c98f6e5d5f3e"}, "logfile": {"src": "hda", "id": "9c12fd6a3ba76792", "uuid": "c3deba55-280e-4a02-bc5c-7777f998fa52"}, "out_accnos": {"src": "hda", "id": "4d003f3f8bfebf53", "uuid": "8dde0258-7d7d-4cee-9ee3-4d5f186b4acb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.slayer(fasta=fasta.dat,reference=self,name=/tmp/saskia/tmpKSDp0 \rp/files/000/dataset_159.dat,search=kmer,window=50,increment=5,match=5,mismatch=- \r4,numwanted=15,parents=3,minsim=90,mincov=70,iters=1000,minbs=90,minsnp=10,diver \rgence=1.007,trim=false,split=false,dereplicate=false,processors=1)\n\nUsing 1 processors.\nChecking sequences from fasta.dat ...\nSorting fastafile according to abundance...Done.\nReading sequences from fasta.dat...Done.\n\nOnly reporting sequence supported by 90% of bootstrapped results.\nProcessing sequence: 32\nIt took 0 secs to check 32 sequences.\n\nOutput File Names: \nfasta.slayer.chimeras\nfasta.slayer.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s ln -s `dirname $(which mothur)`/* . &&  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_158.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_159.dat' alignment.name.dat && ln -s 'None' alignment.group.dat && ln -s 'None' alignment.count.dat &&  echo 'chimera.slayer( fasta=fasta.dat, reference=self, name=/tmp/saskia/tmpKSDp0p/files/000/dataset_159.dat, search=kmer, window=50, increment=5, match=5, mismatch=-4, numwanted=15, parents=3, minsim=90, mincov=70, iters=1000, minbs=90, minsnp=10, divergence=1.007, trim=false, split=false, dereplicate=false, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | ./mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:58:27.298736", "params": {"dereplicate": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"count\": null, \"source\": \"self\", \"group\": null, \"name\": {\"values\": [{\"src\": \"hda\", \"id\": 159}]}, \"__current_case__\": 2}", "dbkey": "\"hg17\"", "options": "{\"trim\": \"false\", \"mincov\": \"70\", \"search\": \"kmer\", \"numwanted\": \"15\", \"increment\": \"5\", \"iters\": \"1000\", \"divergence\": \"1.007\", \"mismatch\": \"-4\", \"minsnp\": \"10\", \"window\": \"50\", \"parents\": \"3\", \"split\": \"false\", \"__current_case__\": 1, \"minsim\": \"90\", \"setby\": \"user\", \"minbs\": \"90\", \"match\": \"5\"}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8976", "id": "b31f4d82ada5e956", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_slayer.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "cd5f25030bbf4788"}, "template|source": "hist", "template|reference": {"src": "hda", "id": "c32d13cb5f20eb1c"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "cd5f25030bbf4788", "uuid": "1e26bb54-6b57-4320-9a90-ff58a5d3684d"}, "reference": {"src": "hda", "id": "c32d13cb5f20eb1c", "uuid": "c08ca8ce-f149-457f-b640-d65b8ffd0a69"}}, "update_time": "2018-02-08T16:58:51.128610", "tool_id": "mothur_chimera_uchime", "outputs": {"out_count": {"src": "hda", "id": "c011a4b8aa5812a2", "uuid": "34e4372e-3ac7-4a13-8dce-eed7ac1cc51a"}, "logfile": {"src": "hda", "id": "33d716567e7a5529", "uuid": "266a88bd-2fe5-4e91-a8f8-92b3dbfd7eb3"}, "out_accnos": {"src": "hda", "id": "b0fc776b5139d032", "uuid": "7c5c28ae-4502-404e-828e-9c8d3d2949b0"}, "uchime.chimeras": {"src": "hda", "id": "c9cd75d91880a01c", "uuid": "69d3f258-8abc-47ba-a723-57a96bdeea7c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.uchime(fasta=fasta.dat,reference=template.reference.dat,minh=0. \r3,mindiv=0.5,xn=8.0,dn=1.4,xa=1.0,chunks=4,minchunk=64,idsmoothwindow=32,maxp=2, \rminlen=10,maxlen=10000,skipgaps=true,skipgaps2=true,dereplicate=false,chimealns= \rfalse,processors=1)\n\nUsing 1 processors.\n/home/saskia/miniconda3/envs/__mothur@1.39.5/bin/mothuruchime file does not exist. Checking path... \nFound uchime in your path, using /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/uchime\n\nuchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\nChecking sequences from fasta.dat ...\nuchime v4.2.40\nby Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\n\nIt took 0 secs to check 3 sequences. 1 chimeras were found.\n\nOutput File Names: \nfasta.ref.uchime.chimeras\nfasta.ref.uchime.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_163.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_164.dat' template.reference.dat &&  echo 'chimera.uchime( fasta=fasta.dat, reference=template.reference.dat, minh=0.3, mindiv=0.5, xn=8.0, dn=1.4, xa=1.0, chunks=4, minchunk=64, idsmoothwindow=32, maxp=2, minlen=10, maxlen=10000, skipgaps=true, skipgaps2=true, dereplicate=false, chimealns=false, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log 2>&1", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:58:47.885084", "params": {"dn": "\"1.4\"", "dereplicate": "\"false\"", "minh": "\"0.3\"", "minchunk": "\"64\"", "xn": "\"8.0\"", "skipgaps2": "\"true\"", "minlen": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "maxp": "\"2\"", "xa": "\"1.0\"", "skipgaps": "\"true\"", "dbkey": "\"hg17\"", "maxlen": "\"10000\"", "mindiv": "\"0.5\"", "template": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 164}]}, \"__current_case__\": 1}", "chunks": "\"4\"", "idsmoothwindow": "\"32\"", "alignment": "{\"ucl\": \"global\", \"__current_case__\": 0}", "chimealns": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n00:00  31Mb    0.1% Reading fasta.dat.uchime_formatted\r00:00  31Mb    0.1% Reading fasta.dat.uchime_formatted\r\nWARNING: Ignoring gaps in FASTA file 'fasta.dat.uchime_formatted'\n00:00  31Mb  100.0% Reading fasta.dat.uchime_formatted\r\n00:00  31Mb 3 sequences                               \n00:00  32Mb    0.1% Reading template.reference.dat\r00:00  32Mb    0.1% Reading template.reference.dat\r00:00  32Mb  100.0% Reading template.reference.dat\r\n00:00  32Mb 32 sequences                          \n00:00  32Mb   33.3% 0/0 chimeras found (0.0%)\r00:00  32Mb  100.0% 1/2 chimeras found (33.3%)\r\n", "job_metrics": [], "model_class": "Job", "external_id": "9098", "id": "87dca8aa4ee9d3de", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_uchime.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "89c96313ae93d0a8"}, "template|source": "self"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "89c96313ae93d0a8", "uuid": "5fd9ba22-20a6-490e-8491-5b27dc07ab63"}}, "update_time": "2018-02-08T16:59:13.498829", "tool_id": "mothur_chimera_uchime", "outputs": {"logfile": {"src": "hda", "id": "e78965a26b62ba53", "uuid": "b2eaa7cc-4350-4ca0-b3bf-3078bd04e439"}, "out_accnos": {"src": "hda", "id": "6fbaeb4019cd0c5e", "uuid": "68914b1b-7095-49ba-b798-c947f7d0315c"}, "uchime.chimeras": {"src": "hda", "id": "8b9818d7842d6e75", "uuid": "377b8759-870f-4f64-ac84-5c8c55c7be7a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.uchime(fasta=fasta.dat,reference=self,abskew=1.9,minh=0.3,mindi \rv=0.5,xn=8.0,dn=1.4,xa=1.0,chunks=4,minchunk=64,idsmoothwindow=32,maxp=2,minlen= \r10,maxlen=10000,skipgaps=true,skipgaps2=true,dereplicate=false,chimealns=false,p \rrocessors=1)\n\nUsing 1 processors.\n/home/saskia/miniconda3/envs/__mothur@1.39.5/bin/mothuruchime file does not exist. Checking path... \nFound uchime in your path, using /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/uchime\n\nuchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\nChecking sequences from fasta.dat ...\n\nNo namesfile given, running unique.seqs command to generate one.\n\n/******************************************/\nRunning command: unique.seqs(fasta=fasta.dat)\n10\t9\n\nOutput File Names: \nfasta.names\nfasta.unique.dat\n\n/******************************************/\nuchime v4.2.40\nby Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\n\nIt took 0 secs to check 9 sequences. 0 chimeras were found.\n\nOutput File Names: \nfasta.denovo.uchime.chimeras\nfasta.denovo.uchime.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_169.dat' fasta.dat && ln -s 'None' template.count.dat && ln -s 'None' template.group.dat &&  echo 'chimera.uchime( fasta=fasta.dat, reference=self, abskew=1.9, minh=0.3, mindiv=0.5, xn=8.0, dn=1.4, xa=1.0, chunks=4, minchunk=64, idsmoothwindow=32, maxp=2, minlen=10, maxlen=10000, skipgaps=true, skipgaps2=true, dereplicate=false, chimealns=false, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log 2>&1", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:59:10.293294", "params": {"dn": "\"1.4\"", "dereplicate": "\"false\"", "minh": "\"0.3\"", "minchunk": "\"64\"", "xn": "\"8.0\"", "skipgaps2": "\"true\"", "minlen": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "maxp": "\"2\"", "xa": "\"1.0\"", "skipgaps": "\"true\"", "dbkey": "\"hg17\"", "maxlen": "\"10000\"", "mindiv": "\"0.5\"", "template": "{\"count\": null, \"source\": \"self\", \"group\": null, \"abskew\": \"1.9\", \"__current_case__\": 2}", "chunks": "\"4\"", "idsmoothwindow": "\"32\"", "alignment": "{\"ucl\": \"global\", \"__current_case__\": 0}", "chimealns": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n00:00  31Mb    0.1% Reading fasta.temp\r00:00  31Mb    0.1% Reading fasta.temp\r\nWARNING: Ignoring gaps in FASTA file 'fasta.temp'\n00:00  31Mb  100.0% Reading fasta.temp\r\n00:00  31Mb 9 sequences               \n00:00  15Mb   11.1% 0/0 chimeras found (0.0%)\r00:00  15Mb  100.0% 0/8 chimeras found (0.0%)\r\n", "job_metrics": [], "model_class": "Job", "external_id": "9189", "id": "a94ebc130565c5b1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_uchime.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "b3dbb33ff37f6ca1"}, "chimealns": true, "template|source": "hist", "template|reference": {"src": "hda", "id": "2ff97a24d56d906f"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "b3dbb33ff37f6ca1", "uuid": "b5bcf445-3dac-4b1d-a8c4-9aad3d469bf9"}, "reference": {"src": "hda", "id": "2ff97a24d56d906f", "uuid": "cfd51060-1f31-447d-a1ea-948717638e70"}}, "update_time": "2018-02-08T16:59:39.670466", "tool_id": "mothur_chimera_uchime", "outputs": {"out_count": {"src": "hda", "id": "e8a2248405ed0640", "uuid": "be2c0c51-cce2-4283-880c-db5b089e59fa"}, "logfile": {"src": "hda", "id": "7de538ea4ff833f8", "uuid": "30ca70fd-4cf8-423b-9ccc-d868063ad1de"}, "out_accnos": {"src": "hda", "id": "3917f5d5eeab2729", "uuid": "a351d373-127a-4808-a5ba-58cf7e7fd433"}, "out_alns": {"src": "hda", "id": "1be3f70673e658a4", "uuid": "1c5ceafc-ee74-4abe-8743-5423286b75b8"}, "uchime.chimeras": {"src": "hda", "id": "a6edf8654f66f4d6", "uuid": "7a10a59e-a7d3-4093-b364-5d92e7978df3"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chimera.uchime(fasta=fasta.dat,reference=template.reference.dat,minh=0. \r3,mindiv=0.5,xn=8.0,dn=1.4,xa=1.0,chunks=4,minchunk=64,idsmoothwindow=32,maxp=2, \rminlen=10,maxlen=10000,skipgaps=true,skipgaps2=true,dereplicate=false,chimealns= \rtrue,processors=1)\n\nUsing 1 processors.\n/home/saskia/miniconda3/envs/__mothur@1.39.5/bin/mothuruchime file does not exist. Checking path... \nFound uchime in your path, using /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/uchime\n\nuchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\nChecking sequences from fasta.dat ...\nuchime v4.2.40\nby Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\n\nIt took 0 secs to check 3 sequences. 1 chimeras were found.\n\nOutput File Names: \nfasta.ref.uchime.chimeras\nfasta.ref.uchime.accnos\nfasta.ref.uchime.alns\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_173.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_174.dat' template.reference.dat &&  echo 'chimera.uchime( fasta=fasta.dat, reference=template.reference.dat, minh=0.3, mindiv=0.5, xn=8.0, dn=1.4, xa=1.0, chunks=4, minchunk=64, idsmoothwindow=32, maxp=2, minlen=10, maxlen=10000, skipgaps=true, skipgaps2=true, dereplicate=false, chimealns=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log 2>&1", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T16:59:36.186909", "params": {"dn": "\"1.4\"", "dereplicate": "\"false\"", "minh": "\"0.3\"", "minchunk": "\"64\"", "xn": "\"8.0\"", "skipgaps2": "\"true\"", "minlen": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "maxp": "\"2\"", "xa": "\"1.0\"", "skipgaps": "\"true\"", "dbkey": "\"hg17\"", "maxlen": "\"10000\"", "mindiv": "\"0.5\"", "template": "{\"source\": \"hist\", \"reference\": {\"values\": [{\"src\": \"hda\", \"id\": 174}]}, \"__current_case__\": 1}", "chunks": "\"4\"", "idsmoothwindow": "\"32\"", "alignment": "{\"ucl\": \"global\", \"__current_case__\": 0}", "chimealns": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n00:00  31Mb    0.1% Reading fasta.dat.uchime_formatted\r00:00  31Mb    0.1% Reading fasta.dat.uchime_formatted\r\nWARNING: Ignoring gaps in FASTA file 'fasta.dat.uchime_formatted'\n00:00  31Mb  100.0% Reading fasta.dat.uchime_formatted\r\n00:00  31Mb 3 sequences                               \n00:00  32Mb    0.1% Reading template.reference.dat\r00:00  32Mb    0.1% Reading template.reference.dat\r00:00  32Mb  100.0% Reading template.reference.dat\r\n00:00  32Mb 32 sequences                          \n00:00  32Mb   33.3% 0/0 chimeras found (0.0%)\r00:00  32Mb  100.0% 1/2 chimeras found (33.3%)\r\n", "job_metrics": [], "model_class": "Job", "external_id": "9321", "id": "945d4aa2c8920004", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chimera_uchime.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "df2cbca38520d0f1"}, "name": {"src": "hda", "id": "26f324d382d6d8c1"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "df2cbca38520d0f1", "uuid": "1f74f4c9-d4fc-46cd-a4ad-6fb3730b4472"}, "name": {"src": "hda", "id": "26f324d382d6d8c1", "uuid": "0944afd4-1adc-40bc-abf9-65e7952db00c"}}, "update_time": "2018-02-08T17:00:13.194061", "tool_id": "mothur_chop_seqs", "outputs": {"logfile": {"src": "hda", "id": "168b8fc92b5c87b9", "uuid": "98e386fc-76dc-4d81-a1ff-9c56fd20b90a"}, "out_fasta": {"src": "hda", "id": "8877579cefa7ba1d", "uuid": "97deef1f-9c02-4dde-86cc-b5a06a207a90"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > chop.seqs(fasta=fasta.dat,numbases=10,keep=front,countgaps=false,short= \rfalse,name=name.dat,processors=1)\n\nUsing 1 processors.\n10\n\nOutput File Names: \nfasta.chop.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_180.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_181.dat' name.dat && ln -s 'None' group.dat && ln -s 'None' count.dat &&  echo 'chop.seqs( fasta=fasta.dat, numbases=10, keep=front, countgaps=false, short=false, name=name.dat, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:00:10.059551", "params": {"count": "null", "short": "\"false\"", "group": "null", "countgaps": "\"false\"", "dbkey": "\"hg17\"", "keep": "\"front\"", "numbases": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9437", "id": "f1e243926043ec87", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_chop_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"tax|source": "hist", "tax|taxonomy": {"src": "hda", "id": "6f4bdab7a73c92f2"}, "otu": {"src": "hda", "id": "f28875befd5fbf72"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "6f4bdab7a73c92f2", "uuid": "697b7231-c675-4892-8fd9-b834494f696b"}, "otu": {"src": "hda", "id": "f28875befd5fbf72", "uuid": "b964b877-996d-4a03-b9aa-4e1d117702b1"}}, "update_time": "2018-02-08T17:00:32.931798", "tool_id": "mothur_classify_otu", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "3b3b4832b2563c85", "uuid": "bda53660-3c27-4d8d-8b4b-d247ef5b7118"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "c786be9a5c4573e3", "uuid": "e16c1b48-9ead-4458-99e3-31f258779006"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "2d6c63bdf033511b", "uuid": "39b45b1d-7ebb-4a80-b5ab-742caf969874"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "f2fbab8d8d8f0547", "uuid": "7c56cf9b-045c-47a3-b98a-0aa0c93b7acb"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "da62383fb67fc13a", "uuid": "6e6df4ea-9ce0-4f4c-b107-4d9386add82c"}, "__new_primary_file_unique|0.16__": {"src": "hda", "id": "10a6a0683c3e243b", "uuid": "80b036be-5867-48cb-88f4-40ce7344bb63"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "6fb508dbe1736155", "uuid": "2e569b9d-2044-4a05-8838-6ea41802ff58"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "ce239e512e8f2197", "uuid": "40ba3095-2425-4eff-89ea-6374a45740b9"}, "__new_primary_file_unique|0.15__": {"src": "hda", "id": "c6c2b27cd5eb370b", "uuid": "77e71211-c70f-4457-8d94-a4ed4aa5482e"}, "__new_primary_file_unique|0.08__": {"src": "hda", "id": "6fccc2792c7809ba", "uuid": "18655ff0-6f1c-4fbd-a36c-914bc55f2f3e"}, "__new_primary_file_unique|0.14__": {"src": "hda", "id": "2c1f3fe730d02717", "uuid": "146c2dda-42f7-4c98-82ce-9c9648eaaac7"}, "__new_primary_file_unique|0.13__": {"src": "hda", "id": "01949e60fe484dc7", "uuid": "8a9200bb-0cdf-4781-93c3-f4a7d0ff0dcc"}, "__new_primary_file_unique|0.09__": {"src": "hda", "id": "06bb318fcaf8f1eb", "uuid": "d5735185-f59a-467a-8c8f-fc0acf2a2038"}, "__new_primary_file_unique|0.12__": {"src": 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"3b3bdb52-fc24-419e-9e43-5c548056c18f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.otu(list=otu.dat,taxonomy=tax.taxonomy.dat,basis=otu,probs=tru \re,persample=false,cutoff=60)\nunique\t96\n[WARNING]: U68667 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68688 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file.  I will not include it in the consensus.\n0.01\t93\n[WARNING]: U68688 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68667 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy f\n..\n.\n[WARNING]: U68641 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file.  I will not include it in the consensus.\n0.55\t1\n[WARNING]: U68688 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68667 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file.  I will not include it in the consensus.\n\nOutput File Names: \notu.unique.cons.taxonomy\notu.unique.cons.tax.summary\notu.0.01.cons.taxonomy\notu.0.01.cons.tax.summary\notu.0.02.cons.taxonomy\notu.0.02.cons.tax.summary\notu.0.03.cons.taxonomy\notu.0.03.cons.tax.summary\notu.0.04.cons.taxonomy\notu.0.04.cons.tax.summary\notu.0.05.cons.taxonomy\notu.0.05.cons.tax.summary\notu.0.06.cons.taxonomy\notu.0.06.cons.tax.summary\notu.0.07.cons.taxonomy\notu.0.07.cons.tax.summary\notu.0.08.cons.taxonomy\notu.0.08.cons.tax.summary\notu.0.09.cons.taxonomy\notu.0.09.cons.tax.summary\notu.0.10.cons.taxonomy\notu.0.10.cons.tax.summary\notu.0.11.cons.taxonomy\notu.0.11.cons.tax.summary\notu.0.12.cons.taxonomy\notu.0.12.cons.tax.summary\notu.0.13.cons.taxonomy\notu.0.13.cons.tax.summary\notu.0.14.cons.taxonomy\notu.0.14.cons.tax.summary\notu.0.15.cons.taxonomy\notu.0.15.cons.tax.summary\notu.0.16.cons.taxonomy\notu.0.16.cons.tax.summary\notu.0.17.cons.taxonomy\notu.0.17.cons.tax.summary\notu.0.18.cons.taxonomy\notu.0.18.cons.tax.summary\notu.0.19.cons.taxonomy\notu.0.19.cons.tax.summary\notu.0.20.cons.taxonomy\notu.0.20.cons.tax.summary\notu.0.21.cons.taxonomy\notu.0.21.cons.tax.summary\notu.0.22.cons.taxonomy\notu.0.22.cons.tax.summary\notu.0.23.cons.taxonomy\notu.0.23.cons.tax.summary\notu.0.24.cons.taxonomy\notu.0.24.cons.tax.summary\notu.0.25.cons.taxonomy\notu.0.25.cons.tax.summary\notu.0.26.cons.taxonomy\notu.0.26.cons.tax.summary\notu.0.27.cons.taxonomy\notu.0.27.cons.tax.summary\notu.0.29.cons.taxonomy\notu.0.29.cons.tax.summary\notu.0.32.cons.taxonomy\notu.0.32.cons.tax.summary\notu.0.33.cons.taxonomy\notu.0.33.cons.tax.summary\notu.0.36.cons.taxonomy\notu.0.36.cons.tax.summary\notu.0.38.cons.taxonomy\notu.0.38.cons.tax.summary\notu.0.41.cons.taxonomy\notu.0.41.cons.tax.summary\notu.0.45.cons.taxonomy\notu.0.45.cons.tax.summary\notu.0.55.cons.taxonomy\notu.0.55.cons.tax.summary\n\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 3528 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_184.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_185.dat' tax.taxonomy.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && ln -s 'None' group.dat &&  echo 'classify.otu( list=otu.dat, taxonomy=tax.taxonomy.dat, basis=otu, probs=true, persample=false, cutoff=60 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:00:25.557457", "params": {"count": "null", "cutoff": "\"60\"", "group": "null", "name": "null", "basis": "\"otu\"", "tax": "{\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 185}]}}", "dbkey": "\"hg17\"", "label": "null", "persample": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "probs": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9552", "id": "19ec6936a7590160", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_otu.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"tax|source": "hist", "label": ["unique", "0.05", "0.18"], "tax|taxonomy": {"src": "hda", "id": "3ecde483422ba55d"}, "otu": {"src": "hda", "id": "14e20f44bf5d2d72"}, "name": {"src": "hda", "id": "41b140d702d99e07"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "3ecde483422ba55d", "uuid": "33feb10f-4177-4489-b970-66fc6003bfe6"}, "name": {"src": "hda", "id": "41b140d702d99e07", "uuid": "f1f2dffb-4746-4ada-874b-c73b5608005d"}, "otu": {"src": "hda", "id": "14e20f44bf5d2d72", "uuid": "bfd08ef0-ab87-4f1b-b5a8-ff566db8e822"}}, "update_time": "2018-02-08T17:01:08.949778", "tool_id": "mothur_classify_otu", "outputs": {"__new_primary_file_unique|unique__": {"src": "hda", "id": "daf78d18ceb29125", "uuid": "b556847d-9014-4648-8be2-855a3334b841"}, "logfile": {"src": "hda", "id": "0e8c18395d13c78f", "uuid": "06734564-dbf7-41b7-a2ea-8bc0c717029d"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "5e8952dd122908bb", "uuid": "b5ed355a-7e41-4d91-a152-ba11da766200"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "7cd46ccec257d13d", "uuid": "4b444b6f-7a24-4cb6-8fb2-02221aecf0a9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.otu(list=otu.dat,taxonomy=tax.taxonomy.dat,name=name.dat,label \r=unique-0.05-0.18,basis=otu,probs=true,persample=false,cutoff=60)\nunique\t96\nU68667 is not in your taxonomy file.  I will not include it in the consensus.\nU68641 is not in your taxonomy file.  I will not include it in the consensus.\nU68620 is not in your taxonomy file.  I will not include it in the consensus.\nU68618 is not in your taxonomy file.  I will not include it in the consensus.\nU68663 is not in your taxonomy file.  I will not include it in the consensus.\nU68662 is not in your taxonomy file.  I will not include it in the consensus.\nU68661 is not in your taxonomy file.  I will not include it in the consensus.\nU68660 is not in your taxonomy file.  I will not include it in the consensus.\nU68659 is not in your taxonomy file.  I will not include it in the consensus.\nU68658 is not in your taxonomy file.  I will not include it in the consensus.\nU68657 is not in your taxonomy file.  I will not include it in the consensus.\nU68656 is not in your taxonomy file.  I will not include it in the consensus.\nU68655 is not in your taxonomy file.  I will not include it in the consensus.\nU68654 is not in your taxonomy file.  I will not include it in the consensus.\nU68653 is not in your taxonomy file.  I will not include it in the consensus.\nU68652 is not in your taxonomy file.  I will not include it in the consensus.\nU68651 is not in your taxonomy file.  I will not include it in the consensus.\nU68649 is not in your taxonomy file.  I will not include it in the consensus.\nU68648 is not in your taxonomy file.  I will not include it in the consensus.\nU68647 is not in your taxonomy file.  I will not include it in the consensus.\nU68646 is not in your taxonomy file.  I will not include it in the consensus.\nU68645 is not in your taxonomy file.  I will not include it in the consensus.\nU68644 is not in your taxonomy file.  I will not include it in the consensus.\nU68643 is not in your taxonomy file.  I will not include it in the consensus.\nU68642 is not in your taxonomy file.  I will not include it in the consensus.\nU68640 is not in your taxonomy file.  I will not include it in the consensus.\nU68639 is not in your taxonomy file.  I will not include it in the consensus.\nU68688 is not in your taxonomy file.  I will not include it in the consensus.\nU68687 is not in your taxonomy file.  I will not include it in the consensus.\nU68686 is not in your taxonomy file.  I will not include it in the consensus.\nU68685 is not in your taxonomy file.  I will not include it in the consensus.\nU68684 is not in your taxonomy file.  I will not include it in the consensus.\nU68683 is not in your taxonomy file.  I will not include it in the consensus.\nU68682 is not in your taxonomy file.  I will not include it in the consensus.\nU68681 is not in your taxonomy file.  I will not include it in the consensus.\nU68680 is not in your taxonomy file.  I will not include it in the consensus.\nU68679 is not in your taxonomy file.  I will not include it in the consensus.\nU68678 is not in your taxonomy file.  I will not include it in the consensus.\nU68677 is not in your taxonomy file.  I will not include it in the consensus.\nU68676 is not in your taxonomy file.  I will not include it in the consensus.\nU68675 is not in your taxonomy file.  I will not include it in the consensus.\nU68674 is not in your taxonomy file.  I will not include it in the consensus.\nU68673 is not in your taxonomy file.  I will not include it in the consensus.\nU68672 is not in your taxonomy file.  I will not include it in the consensus.\nU68671 is not in your taxonomy file.  I will not include it in the consensus.\nU68670 is not in your taxonomy file.  I will not include it in the consensus.\nU68669 is not in your taxonomy file.  I will not include it in the consensus.\nU68668 is not in your taxonomy file.  I will not include it in the consensus.\nU68666 is not in your taxonomy file.  I will not include it in the consensus.\nU68665 is not in your taxonomy file.  I will not include it in the consensus.\nU68664 is not in your taxonomy file.  I will not include it in the consensus.\nU68613 is not in your taxonomy file.  I will not include it in the consensus.\nU68612 is not in your taxonomy file.  I will not include it in the consensus.\nU68611 is not in your taxonomy file.  I will not include it in the consensus.\nU68610 is not in your taxonomy file.  I will not include it in the consensus.\nU68609 is not in your taxonomy file.  I will not include it in the consensus.\nU68608 is not in your taxonomy file.  I will not include it in the consensus.\nU68607 is not in your taxonomy file.  I will not include it in the consensus.\nU68606 is not in your taxonomy file.  I will not include it in the consensus.\nU68605 is not in your taxonomy file.  I will not include it in the consensus.\nU68603 is not in your taxonomy file.  I will not include it in the consensus.\nU68602 is not in your taxonomy file.  I will not include it in the consensus.\nU68601 is not in your taxonomy file.  I will not include it in the consensus.\nU68600 is not in your taxonomy file.  I will not include it in the consensus.\nU68599 is not in your taxonomy file.  I will not include it in the consensus.\nU68598 is not in your taxonomy file.  I will not include it in the consensus.\nU68597 is not in your taxonomy file.  I will not include it in the consensus.\nU68596 is not in your taxonomy file.  I will not include it in the consensus.\nU68595 is not in your taxonomy file.  I will not include it in the consensus.\nU68594 is not in your taxonomy file.  I will not include it in the consensus.\nU68593 is not in your taxonomy file.  I will not include it in the consensus.\nU68592 is not in your taxonomy file.  I will not include it in the consensus.\nU68591 is not in your taxonomy file.  I will not include it in the consensus.\nU68590 is not in your taxonomy file.  I will not include it in the consensus.\nU68589 is not in your taxonomy file.  I will not include it in the consensus.\nU68638 is not in your taxonomy file.  I will not include it in the consensus.\nU68637 is not in your taxonomy file.  I will not include it in the consensus.\nU68636 is not in your taxonomy file.  I will not include it in the consensus.\nU68635 is not in your taxonomy file.  I will not include it in the consensus.\nU68634 is not in your taxonomy file.  I will not include it in the consensus.\nU68633 is not in your taxonomy file.  I will not include it in the consensus.\nU68632 is not in your taxonomy file.  I will not include it in the consensus.\nU68631 is not in your taxonomy file.  I will not include it in the consensus.\nU68630 is not in your taxonomy file.  I will not include it in the consensus.\nU68629 is not in your taxonomy file.  I will not include it in the consensus.\nU68628 is not in your taxonomy file.  I will not include it in the consensus.\nU68627 is not in your taxonomy file.  I will not include it in the consensus.\nU68626 is not in your taxonomy file.  I will not include it in the consensus.\nU68625 is not in your taxonomy file.  I will not include it in the consensus.\nU68624 is not in your taxonomy file.  I will not include it in the consensus.\nU68623 is not in your taxonomy file.  I will not include it in the consensus.\nU68622 is not in your taxonomy file.  I will not include it in the consensus.\nU68621 is not in your taxonomy file.  I will not include it in the consensus.\nU68619 is not in your taxonomy file.  I will not include it in the consensus.\nU68617 is not in your taxonomy file.  I will not include it in the consensus.\nU68616 is not in your taxonomy file.  I will not include it in the consensus.\nU68615 is not in your taxonomy file.  I will not include it in the consensus.\nU68614 is not in your taxonomy file.  I will not include it in the consensus.\n0.05\t78\nU68688 is not in your taxonomy file.  I will not include it in the consensus.\nU68665 is not in your taxonomy file.  I will not include it in the consensus.\nU68679 is not in your taxonomy file.  I will not include it in the consensus.\nU68663 is not in your taxonomy file.  I will not include it in the consensus.\nU68658 is not in your taxonomy file.  I will not include it in the consensus.\nU68638 is not in your taxonomy file.  I will not include it in the consensus.\nU68620 is not in your taxonomy file.  I will not include it in the consensus.\nU68618 is not in your taxonomy file.  I will not include it in the consensus.\nU68683 is not in your taxonomy file.  I will not include it in the consensus.\nU68652 is not in your taxonomy file.  I will not include it in the consensus.\nU68610 is not in your taxonomy file.  I will not include it in the consensus.\nU68673 is not in your taxonomy file.  I will not include it in the consensus.\nU68667 is not in your taxonomy file.  I will not include it in the consensus.\nU68641 is not in your taxonomy file.  I will not include it in the consensus.\nU68636 is not in your taxonomy file.  I will not include it in the consensus.\nU68631 is not in your taxonomy file.  I will not include it in the consensus.\nU68637 is not in your taxonomy file.  I will not include it in the consensus.\nU68602 is not in your taxonomy file.  I will not include it in the consensus.\nU68628 is not in your taxonomy file.  I will not include it in the consensus.\nU68601 is not in your taxonomy file.  I will not include it in the consensus.\nU68614 is not in your taxonomy file.  I will not include it in the consensus.\nU68596 is not in your taxonomy file.  I will not include it in the consensus.\nU68666 is not in your taxonomy file.  I will not include it in the consensus.\nU68595 is not in your taxonomy file.  I will not include it in the consensus.\nU68672 is not in your taxonomy file.  I will not include it in the consensus.\nU68621 is not in your taxonomy file.  I will not include it in the consensus.\nU68686 is not in your taxonomy file.  I will not include it in the consensus.\nU68635 is not in your taxonomy file.  I will not include it in the consensus.\nU68678 is not in your taxonomy file.  I will not include it in the consensus.\nU68619 is not in your taxonomy file.  I will not include it in the consensus.\nU68680 is not in your taxonomy file.  I will not include it in the consensus.\nU68615 is not in your taxonomy file.  I will not include it in the consensus.\nU68681 is not in your taxonomy file.  I will not include it in the consensus.\nU68677 is not in your taxonomy file.  I will not include it in the consensus.\nU68654 is not in your taxonomy file.  I will not include it in the consensus.\nU68653 is not in your taxonomy file.  I will not include it in the consensus.\nU68651 is not in your taxonomy file.  I will not include it in the consensus.\nU68649 is not in your taxonomy file.  I will not include it in the consensus.\nU68648 is not in your taxonomy file.  I will not include it in the consensus.\nU68647 is not in your taxonomy file.  I will not include it in the consensus.\nU68646 is not in your taxonomy file.  I will not include it in the consensus.\nU68645 is not in your taxonomy file.  I will not include it in the consensus.\nU68685 is not in your taxonomy file.  I will not include it in the consensus.\nU68644 is not in your taxonomy file.  I will not include it in the consensus.\nU68643 is not in your taxonomy file.  I will not include it in the consensus.\nU68642 is not in your taxonomy file.  I will not include it in the consensus.\nU68640 is not in your taxonomy file.  I will not include it in the consensus.\nU68639 is not in your taxonomy file.  I will not include it in the consensus.\nU68687 is not in your taxonomy file.  I will not include it in the consensus.\nU68676 is not in your taxonomy file.  I will not include it in the consensus.\nU68675 is not in your taxonomy file.  I will not include it in the consensus.\nU68674 is not in your taxonomy file.  I will not include it in the consensus.\nU68671 is not in your taxonomy file.  I will not include it in the consensus.\nU68670 is not in your taxonomy file.  I will not include it in the consensus.\nU68669 is not in your taxonomy file.  I will not include it in the consensus.\nU68668 is not in your taxonomy file.  I will not include it in the consensus.\nU68664 is not in your taxonomy file.  I will not include it in the consensus.\nU68662 is not in your taxonomy file.  I will not include it in the consensus.\nU68661 is not in your taxonomy file.  I will not include it in the consensus.\nU68660 is not in your taxonomy file.  I will not include it in the consensus.\nU68682 is not in your taxonomy file.  I will not include it in the consensus.\nU68659 is not in your taxonomy file.  I will not include it in the consensus.\nU68684 is not in your taxonomy file.  I will not include it in the consensus.\nU68657 is not in your taxonomy file.  I will not include it in the consensus.\nU68656 is not in your taxonomy file.  I will not include it in the consensus.\nU68655 is not in your taxonomy file.  I will not include it in the consensus.\nU68607 is not in your taxonomy file.  I will not include it in the consensus.\nU68608 is not in your taxonomy file.  I will not include it in the consensus.\nU68600 is not in your taxonomy file.  I will not include it in the consensus.\nU68609 is not in your taxonomy file.  I will not include it in the consensus.\nU68599 is not in your taxonomy file.  I will not include it in the consensus.\nU68606 is not in your taxonomy file.  I will not include it in the consensus.\nU68598 is not in your taxonomy file.  I will not include it in the consensus.\nU68611 is not in your taxonomy file.  I will not include it in the consensus.\nU68612 is not in your taxonomy file.  I will not include it in the consensus.\nU68613 is not in your taxonomy file.  I will not include it in the consensus.\nU68605 is not in your taxonomy file.  I will not include it in the consensus.\nU68616 is not in your taxonomy file.  I will not include it in the consensus.\nU68617 is not in your taxonomy file.  I will not include it in the consensus.\nU68597 is not in your taxonomy file.  I will not include it in the consensus.\nU68603 is not in your taxonomy file.  I will not include it in the consensus.\nU68594 is not in your taxonomy file.  I will not include it in the consensus.\nU68589 is not in your taxonomy file.  I will not include it in the consensus.\nU68634 is not in your taxonomy file.  I will not include it in the consensus.\nU68590 is not in your taxonomy file.  I will not include it in the consensus.\nU68633 is not in your taxonomy file.  I will not include it in the consensus.\nU68632 is not in your taxonomy file.  I will not include it in the consensus.\nU68591 is not in your taxonomy file.  I will not include it in the consensus.\nU68592 is not in your taxonomy file.  I will not include it in the consensus.\nU68630 is not in your taxonomy file.  I will not include it in the consensus.\nU68629 is not in your taxonomy file.  I will not include it in the consensus.\nU68627 is not in your taxonomy file.  I will not include it in the consensus.\nU68626 is not in your taxonomy file.  I will not include it in the consensus.\nU68625 is not in your taxonomy file.  I will not include it in the consensus.\nU68624 is not in your taxonomy file.  I will not include it in the consensus.\nU68623 is not in your taxonomy file.  I will not include it in the consensus.\nU68622 is not in your taxonomy file.  I will not include it in the consensus.\nU68593 is not in your taxonomy file.  I will not include it in the consensus.\n0.18\t31\nU68686 is not in your taxonomy file.  I will not include it in the consensus.\nU68635 is not in your taxonomy file.  I will not include it in the consensus.\nU68613 is not in your taxonomy file.  I will not include it in the consensus.\nU68637 is not in your taxonomy file.  I will not include it in the consensus.\nU68602 is not in your taxonomy file.  I will not include it in the consensus.\nU68678 is not in your taxonomy file.  I will not include it in the consensus.\nU68619 is not in your taxonomy file.  I will not include it in the consensus.\nU68645 is not in your taxonomy file.  I will not include it in the consensus.\nU68673 is not in your taxonomy file.  I will not include it in the consensus.\nU68667 is not in your taxonomy file.  I will not include it in the consensus.\nU68641 is not in your taxonomy file.  I will not include it in the consensus.\nU68598 is not in your taxonomy file.  I will not include it in the consensus.\nU68658 is not in your taxonomy file.  I will not include it in the consensus.\nU68638 is not in your taxonomy file.  I will not include it in the consensus.\nU68620 is not in your taxonomy file.  I will not include it in the consensus.\nU68618 is not in your taxonomy file.  I will not include it in the consensus.\nU68659 is not in your taxonomy file.  I will not include it in the consensus.\nU68624 is not in your taxonomy file.  I will not include it in the consensus.\nU68655 is not in your taxonomy file.  I will not include it in the consensus.\nU68651 is not in your taxonomy file.  I will not include it in the consensus.\nU68640 is not in your taxonomy file.  I will not include it in the consensus.\nU68688 is not in your taxonomy file.  I will not include it in the consensus.\nU68665 is not in your taxonomy file.  I will not include it in the consensus.\nU68679 is not in your taxonomy file.  I will not include it in the consensus.\nU68663 is not in your taxonomy file.  I will not include it in the consensus.\nU68653 is not in your taxonomy file.  I will not include it in the consensus.\nU68676 is not in your taxonomy file.  I will not include it in the consensus.\nU68660 is not in your taxonomy file.  I will not include it in the consensus.\nU68647 is not in your taxonomy file.  I will not include it in the consensus.\nU68626 is not in your taxonomy file.  I will not include it in the consensus.\nU68623 is not in your taxonomy file.  I will not include it in the consensus.\nU68683 is not in your taxonomy file.  I will not include it in the consensus.\nU68652 is not in your taxonomy file.  I will not include it in the consensus.\nU68610 is not in your taxonomy file.  I will not include it in the consensus.\nU68671 is not in your taxonomy file.  I will not include it in the consensus.\nU68666 is not in your taxonomy file.  I will not include it in the consensus.\nU68595 is not in your taxonomy file.  I will not include it in the consensus.\nU68636 is not in your taxonomy file.  I will not include it in the consensus.\nU68631 is not in your taxonomy file.  I will not include it in the consensus.\nU68634 is not in your taxonomy file.  I will not include it in the consensus.\nU68628 is not in your taxonomy file.  I will not include it in the consensus.\nU68601 is not in your taxonomy file.  I will not include it in the consensus.\nU68607 is not in your taxonomy file.  I will not include it in the consensus.\nU68629 is not in your taxonomy file.  I will not include it in the consensus.\nU68617 is not in your taxonomy file.  I will not include it in the consensus.\nU68614 is not in your taxonomy file.  I will not include it in the consensus.\nU68596 is not in your taxonomy file.  I will not include it in the consensus.\nU68684 is not in your taxonomy file.  I will not include it in the consensus.\nU68654 is not in your taxonomy file.  I will not include it in the consensus.\nU68593 is not in your taxonomy file.  I will not include it in the consensus.\nU68649 is not in your taxonomy file.  I will not include it in the consensus.\nU68639 is not in your taxonomy file.  I will not include it in the consensus.\nU68606 is not in your taxonomy file.  I will not include it in the consensus.\nU68682 is not in your taxonomy file.  I will not include it in the consensus.\nU68657 is not in your taxonomy file.  I will not include it in the consensus.\nU68675 is not in your taxonomy file.  I will not include it in the consensus.\nU68627 is not in your taxonomy file.  I will not include it in the consensus.\nU68609 is not in your taxonomy file.  I will not include it in the consensus.\nU68680 is not in your taxonomy file.  I will not include it in the consensus.\nU68615 is not in your taxonomy file.  I will not include it in the consensus.\nU68670 is not in your taxonomy file.  I will not include it in the consensus.\nU68611 is not in your taxonomy file.  I will not include it in the consensus.\nU68648 is not in your taxonomy file.  I will not include it in the consensus.\nU68632 is not in your taxonomy file.  I will not include it in the consensus.\nU68605 is not in your taxonomy file.  I will not include it in the consensus.\nU68597 is not in your taxonomy file.  I will not include it in the consensus.\nU68687 is not in your taxonomy file.  I will not include it in the consensus.\nU68592 is not in your taxonomy file.  I will not include it in the consensus.\nU68685 is not in your taxonomy file.  I will not include it in the consensus.\nU68681 is not in your taxonomy file.  I will not include it in the consensus.\nU68677 is not in your taxonomy file.  I will not include it in the consensus.\nU68669 is not in your taxonomy file.  I will not include it in the consensus.\nU68646 is not in your taxonomy file.  I will not include it in the consensus.\nU68590 is not in your taxonomy file.  I will not include it in the consensus.\nU68644 is not in your taxonomy file.  I will not include it in the consensus.\nU68633 is not in your taxonomy file.  I will not include it in the consensus.\nU68612 is not in your taxonomy file.  I will not include it in the consensus.\nU68600 is not in your taxonomy file.  I will not include it in the consensus.\nU68591 is not in your taxonomy file.  I will not include it in the consensus.\nU68672 is not in your taxonomy file.  I will not include it in the consensus.\nU68621 is not in your taxonomy file.  I will not include it in the consensus.\nU68625 is not in your taxonomy file.  I will not include it in the consensus.\nU68630 is not in your taxonomy file.  I will not include it in the consensus.\nU68622 is not in your taxonomy file.  I will not include it in the consensus.\nU68616 is not in your taxonomy file.  I will not include it in the consensus.\nU68642 is not in your taxonomy file.  I will not include it in the consensus.\nU68643 is not in your taxonomy file.  I will not include it in the consensus.\nU68656 is not in your taxonomy file.  I will not include it in the consensus.\nU68661 is not in your taxonomy file.  I will not include it in the consensus.\nU68662 is not in your taxonomy file.  I will not include it in the consensus.\nU68664 is not in your taxonomy file.  I will not include it in the consensus.\nU68668 is not in your taxonomy file.  I will not include it in the consensus.\nU68674 is not in your taxonomy file.  I will not include it in the consensus.\nU68599 is not in your taxonomy file.  I will not include it in the consensus.\nU68608 is not in your taxonomy file.  I will not include it in the consensus.\nU68603 is not in your taxonomy file.  I will not include it in the consensus.\nU68594 is not in your taxonomy file.  I will not include it in the consensus.\nU68589 is not in your taxonomy file.  I will not include it in the consensus.\n\nOutput File Names: \notu.unique.cons.taxonomy\notu.unique.cons.tax.summary\notu.0.05.cons.taxonomy\notu.0.05.cons.tax.summary\notu.0.18.cons.taxonomy\notu.0.18.cons.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_259.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_261.dat' tax.taxonomy.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_260.dat' name.dat && ln -s 'None' count.dat && ln -s 'None' group.dat &&  echo 'classify.otu( list=otu.dat, taxonomy=tax.taxonomy.dat, name=name.dat, label=unique-0.05-0.18, basis=otu, probs=true, persample=false, cutoff=60 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:01:05.437469", "params": {"count": "null", "cutoff": "\"60\"", "group": "null", "basis": "\"otu\"", "tax": "{\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 261}]}}", "dbkey": "\"hg17\"", "label": "[\"unique\", \"0.05\", \"0.18\"]", "persample": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "probs": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9694", "id": "97f8596e58df898c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_otu.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "a658f0c7b599f85a"}, "tax|source": "hist", "tax|taxonomy": {"src": "hda", "id": "5d952db0f0e41e99"}, "otu": {"src": "hda", "id": "1d5ca124ec943537"}, "label": ["unique", "0.05", "0.18"]}, "job": {"inputs": {"count": {"src": "hda", "id": "a658f0c7b599f85a", "uuid": "7051ce7a-a5d0-4ed9-a13e-7882ad5f7bed"}, "taxonomy": {"src": "hda", "id": "5d952db0f0e41e99", "uuid": "20a3ee2a-4eb1-4153-babd-2de585f13f8e"}, "otu": {"src": "hda", "id": "1d5ca124ec943537", "uuid": "9e4d3e13-6fd2-4c20-acfc-6891473c8bb8"}}, "update_time": "2018-02-08T17:01:41.985823", "tool_id": "mothur_classify_otu", "outputs": {"__new_primary_file_unique|unique__": {"src": "hda", "id": "648ee5580acb394c", "uuid": "968165ec-5a61-489b-9f5a-1c4a44d8209b"}, "logfile": {"src": "hda", "id": "a419613b7d66b4dd", "uuid": "22b5cf38-8021-4ac3-b82a-b3775dc54efc"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "e038b12fcc34712c", "uuid": "46b94bc7-fc22-413a-b0d9-e9fcc3140e56"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "846dc31143592f08", "uuid": "1777501a-5552-444e-b5f1-b8817295f9ea"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.otu(list=otu.dat,taxonomy=tax.taxonomy.dat,count=count.dat,lab \rel=unique-0.05-0.18,basis=otu,probs=true,persample=false,cutoff=60)\nunique\t96\n[WARNING]: U68667 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68688 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file.  I will not include it in the consensus.\n0.05\t78\n[WARNING]: U68688 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68667 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file.  I will not include it in the consensus.\n0.18\t31\n[WARNING]: U68686 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68667 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68688 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file.  I will not include it in the consensus.\n\nOutput File Names: \notu.unique.cons.taxonomy\notu.unique.cons.tax.summary\notu.0.05.cons.taxonomy\notu.0.05.cons.tax.summary\notu.0.18.cons.taxonomy\notu.0.18.cons.tax.summary\n\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 294 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_269.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_271.dat' tax.taxonomy.dat && ln -s 'None' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_270.dat' count.dat && ln -s 'None' group.dat &&  echo 'classify.otu( list=otu.dat, taxonomy=tax.taxonomy.dat, count=count.dat, label=unique-0.05-0.18, basis=otu, probs=true, persample=false, cutoff=60 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:01:37.698586", "params": {"cutoff": "\"60\"", "group": "null", "name": "null", "basis": "\"otu\"", "tax": "{\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 271}]}}", "dbkey": "\"hg17\"", "label": "[\"unique\", \"0.05\", \"0.18\"]", "persample": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "probs": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9833", "id": "2fd653ff8fe916b4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_otu.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"tax|source": "hist", "group": {"src": "hda", "id": "b76e2c1d909ec95b"}, "tax|taxonomy": {"src": "hda", "id": "813e726c1c531093"}, "otu": {"src": "hda", "id": "57d21b82f66bdde1"}, "label": ["unique", "0.05", "0.18"]}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "813e726c1c531093", "uuid": "8f98eaf9-8d3f-4b95-8d5c-2827160af834"}, "group": {"src": "hda", "id": "b76e2c1d909ec95b", "uuid": "b108d363-b53b-4ba9-a5ab-5514370b9031"}, "otu": {"src": "hda", "id": "57d21b82f66bdde1", "uuid": "4b4c9c08-0b9e-4c76-8c65-1bf75ba8a076"}}, "update_time": "2018-02-08T17:02:13.958072", "tool_id": "mothur_classify_otu", "outputs": {"__new_primary_file_unique|unique__": {"src": "hda", "id": "3eabac299c8a6493", "uuid": "9fce3e7c-3d6c-489a-afd1-0157a5edb910"}, "logfile": {"src": "hda", "id": "694613cce11a624b", "uuid": "d6b6fbb4-5321-4709-af2f-e7c17755f3ea"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "4b73dece6b8202b2", "uuid": "8ee4e725-22ba-4778-a6ac-2a0f9b10b8e0"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "8960b7e82c319407", "uuid": "010aef81-9c17-4c7f-9413-ac98a3b10a6c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.otu(list=otu.dat,taxonomy=tax.taxonomy.dat,label=unique-0.05-0 \r.18,group=group.dat,basis=otu,probs=true,persample=false,cutoff=60)\nunique\t96\n[WARNING]: U68667 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68688 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file.  I will not include it in the consensus.\n0.05\t78\n[WARNING]: U68688 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68667 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68686 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file.  I will not include it in the consensus.\n0.18\t31\n[WARNING]: U68686 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68635 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68613 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68637 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68602 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68678 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68619 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68645 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68673 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68667 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68641 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68598 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68658 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68638 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68620 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68618 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68659 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68624 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68655 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68651 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68640 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68688 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68665 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68679 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68663 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68653 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68676 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68660 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68647 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68626 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68623 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68683 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68652 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68610 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68671 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68666 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68595 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68636 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68631 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68634 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68628 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68601 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68607 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68629 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68617 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68614 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68596 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68684 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68654 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68593 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68649 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68639 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68606 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68682 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68657 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68675 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68627 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68609 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68680 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68615 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68670 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68611 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68648 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68632 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68605 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68597 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68687 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68592 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68685 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68681 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68677 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68669 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68646 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68590 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68644 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68633 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68612 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68600 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68591 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68672 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68621 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68625 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68630 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68622 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68616 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68642 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68643 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68656 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68661 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68662 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68664 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68668 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68674 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68599 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68608 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68603 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68594 is not in your taxonomy file.  I will not include it in the consensus.\n[WARNING]: U68589 is not in your taxonomy file.  I will not include it in the consensus.\n\nOutput File Names: \notu.unique.cons.taxonomy\notu.unique.cons.tax.summary\notu.0.05.cons.taxonomy\notu.0.05.cons.tax.summary\notu.0.18.cons.taxonomy\notu.0.18.cons.tax.summary\n\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 294 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_279.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_280.dat' tax.taxonomy.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_281.dat' group.dat &&  echo 'classify.otu( list=otu.dat, taxonomy=tax.taxonomy.dat, label=unique-0.05-0.18, group=group.dat, basis=otu, probs=true, persample=false, cutoff=60 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:02:10.308889", "params": {"count": "null", "cutoff": "\"60\"", "name": "null", "basis": "\"otu\"", "tax": "{\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 280}]}}", "dbkey": "\"hg17\"", "label": "[\"unique\", \"0.05\", \"0.18\"]", "persample": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "probs": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9963", "id": "c0ae89d2a79fffb2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_otu.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment|template": {"src": "hda", "id": "349f287fcb778b99"}, "fasta": {"src": "hda", "id": "0407161672f94bd4"}, "tax|taxonomy": {"src": "hda", "id": "4b1441c8dda2d2fe"}, "alignment|source": "hist", "tax|source2": "hist"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "4b1441c8dda2d2fe", "uuid": "381f807d-770b-42d4-b24a-32d31669b6b9"}, "fasta": {"src": "hda", "id": "0407161672f94bd4", "uuid": "be23beec-f064-475f-b29d-ad87f64cc62f"}, "template": {"src": "hda", "id": "349f287fcb778b99", "uuid": "391175a3-7a7e-4fd8-804a-bcc27d515553"}}, "update_time": "2018-02-08T17:02:47.091134", "tool_id": "mothur_classify_seqs", "outputs": {"tree_sum": {"src": "hda", "id": "377e6a8287fa8b6a", "uuid": "fe77ae40-a1fd-44c7-9b99-30842ebd72aa"}, "logfile": {"src": "hda", "id": "f66e4e467d639b46", "uuid": "0e7a3aee-7e4d-42fe-b662-09330ca5f7db"}, "taxonomy_out": {"src": "hda", "id": "d60bc3c056ce6d02", "uuid": "6376f71e-8f69-4634-8b4a-de2fd2b243b8"}, "tax_summary": {"src": "hda", "id": "513510c2b856e80e", "uuid": "a49b76f5-5eac-4dfb-a188-bafce159c86e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.seqs(fasta=fasta.dat,reference=alignment.template.dat,taxonomy \r=tax.taxonomy.dat,method=wang,ksize=8,iters=100,cutoff=80,probs=true,relabund=fa \rlse,printlevel=-1,processors=1)\n\nUsing 1 processors.\nGenerating search database...    DONE.\nIt took 0 seconds generate search database. \n\nReading in the tax.taxonomy.dat taxonomy...\tDONE.\nCalculating template taxonomy tree...     DONE.\nCalculating template probabilities...     DONE.\nIt took 1 seconds get probabilities. \nClassifying sequences from fasta.dat ...\n[WARNING]: U68596 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68609 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68611 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68614 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68617 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68618 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68627 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68634 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68638 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68640 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68642 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68643 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68651 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68653 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68656 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68657 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68658 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68668 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68669 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68670 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68675 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68677 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68681 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\n[WARNING]: U68682 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.\nProcessing sequence: 98\n\n[WARNING]: mothur reversed some your sequences for a better classification.  If you would like to take a closer look, please check fasta.taxonomy.wang.flip.accnos for the list of the sequences.\n\nIt took 0 secs to classify 98 sequences.\n\n\nIt took 0 secs to create the summary file for 98 sequences.\n\n\nOutput File Names: \nfasta.taxonomy.wang.taxonomy\nfasta.taxonomy.wang.tax.summary\nfasta.taxonomy.wang.flip.accnos\n\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 25 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s `dirname $(which mothur)`/* . &&  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_289.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_290.dat' alignment.template.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_291.dat' tax.taxonomy.dat && ln -s 'None' count.dat && ln -s 'None' name.dat &&  echo 'classify.seqs( fasta=fasta.dat, reference=alignment.template.dat, taxonomy=tax.taxonomy.dat, method=wang, ksize=8, iters=100, cutoff=80, probs=true, relabund=false, printlevel=-1, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | ./mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:02:43.203871", "params": {"count": "null", "name": "null", "relabund": "\"false\"", "tax": "{\"source2\": \"hist\", \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 291}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\"", "classify": "{\"cutoff\": \"80\", \"iters\": \"100\", \"method\": \"wang\", \"ksize\": \"8\", \"__current_case__\": 0, \"probs\": \"true\"}", "printlevel": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 290}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "10110", "id": "20de7af3d288c35f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment|source": "hist", "alignment|template": {"src": "hda", "id": "b09dd54432ee600c"}, "classify|method": "knn", "fasta": {"src": "hda", "id": "25de304670fe7732"}, "tax|taxonomy": {"src": "hda", "id": "d57022ef22692475"}, "tax|source2": "hist"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "d57022ef22692475", "uuid": "c5a22f6a-70ff-4be6-9ba1-539f6d461dc9"}, "fasta": {"src": "hda", "id": "25de304670fe7732", "uuid": "831ee786-6fba-4803-b0ec-193c971e80e0"}, "template": {"src": "hda", "id": "b09dd54432ee600c", "uuid": "d6d8be3f-1709-46c3-a983-664e37ff6a50"}}, "update_time": "2018-02-08T17:03:25.633396", "tool_id": "mothur_classify_seqs", "outputs": {"tree_sum": {"src": "hda", "id": "c64bfc8445bed47e", "uuid": "678f639a-1732-4d98-8d91-e026ba091ebb"}, "logfile": {"src": "hda", "id": "7528831c3de506aa", "uuid": "9da71a0b-5901-4861-b9af-a7d50b40fd6d"}, "taxonomy_out": {"src": "hda", "id": "9b36a3aa47b79bf2", "uuid": "d0682327-05f1-48b6-8135-0888ec93e2ea"}, "tax_summary": {"src": "hda", "id": "14f44a11533277c1", "uuid": "754d8fee-d74e-402b-a9bd-e38b3c9b05d9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.seqs(fasta=fasta.dat,reference=alignment.template.dat,taxonomy \r=tax.taxonomy.dat,method=knn,numwanted=10,search=kmer,ksize=8,relabund=false,pri \rntlevel=-1,processors=1)\n\nUsing 1 processors.\nGenerating search database...    DONE.\nIt took 0 seconds generate search database. \n\nReading in the tax.taxonomy.dat taxonomy...\tDONE.\nClassifying sequences from fasta.dat ...\nProcessing sequence: 98\n\nIt took 0 secs to classify 98 sequences.\n\n\nIt took 0 secs to create the summary file for 98 sequences.\n\n\nOutput File Names: \nfasta.taxonomy.knn.taxonomy\nfasta.taxonomy.knn.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s `dirname $(which mothur)`/* . &&  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_296.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_297.dat' alignment.template.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_298.dat' tax.taxonomy.dat && ln -s 'None' count.dat && ln -s 'None' name.dat &&  echo 'classify.seqs( fasta=fasta.dat, reference=alignment.template.dat, taxonomy=tax.taxonomy.dat, method=knn, numwanted=10, search=kmer, ksize=8, relabund=false, printlevel=-1, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | ./mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:03:21.352750", "params": {"count": "null", "name": "null", "relabund": "\"false\"", "tax": "{\"source2\": \"hist\", \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 298}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\"", "classify": "{\"search\": {\"__current_case__\": 0, \"algorithm\": \"kmer\", \"ksize\": \"8\"}, \"numwanted\": \"10\", \"method\": \"knn\", \"__current_case__\": 1}", "printlevel": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 297}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "10262", "id": "69ce05044577833e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment|source": "hist", "alignment|template": {"src": "hda", "id": "266b4c416078dc76"}, "classify|method": "knn", "classify|search|algorithm": "blast", "fasta": {"src": "hda", "id": "266b4c416078dc76"}, "tax|taxonomy": {"src": "hda", "id": "0b62b0b7271d572a"}, "tax|source2": "hist"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "0b62b0b7271d572a", "uuid": "40100a80-787e-42c4-9675-299ce099136f"}, "fasta": {"src": "hda", "id": "266b4c416078dc76", "uuid": "b7c393c3-fcd3-4602-8d08-19c7b41c1c11"}, "template": {"src": "hda", "id": "266b4c416078dc76", "uuid": "b7c393c3-fcd3-4602-8d08-19c7b41c1c11"}}, "update_time": "2018-02-08T17:04:00.015489", "tool_id": "mothur_classify_seqs", "outputs": {"tree_sum": {"src": "hda", "id": "044df8528177c496", "uuid": "0f333d2b-e98f-4c1d-9885-b9442a00d0ad"}, "logfile": {"src": "hda", "id": "8543024575f6f30b", "uuid": "94d5ad8d-bac4-4263-9369-41a64e40fb91"}, "taxonomy_out": {"src": "hda", "id": "74219090cb2d0112", "uuid": "10a61d0e-97a8-4051-8e84-49992c7ef157"}, "tax_summary": {"src": "hda", "id": "c8288be11b30d2bc", "uuid": "336d67d8-5c97-4c99-852b-a60d956a0402"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.seqs(fasta=fasta.dat,reference=alignment.template.dat,taxonomy \r=tax.taxonomy.dat,method=knn,numwanted=10,search=blast,match=1,mismatch=-1,gapop \ren=-2,gapextend=-1,relabund=false,printlevel=-1,processors=1)\n\nUsing 1 processors.\nGenerating search database...    DONE.\nIt took 0 seconds generate search database. \n\nReading in the tax.taxonomy.dat taxonomy...\tDONE.\nClassifying sequences from fasta.dat ...\nProcessing sequence: 100\nProcessing sequence: 200\nProcessing sequence: 242\n\nIt took 2 secs to classify 242 sequences.\n\n\nIt took 0 secs to create the summary file for 242 sequences.\n\n\nOutput File Names: \nfasta.taxonomy.knn.taxonomy\nfasta.taxonomy.knn.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s `dirname $(which mothur)`/* . &&  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_304.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_304.dat' alignment.template.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_305.dat' tax.taxonomy.dat && ln -s 'None' count.dat && ln -s 'None' name.dat &&  echo 'classify.seqs( fasta=fasta.dat, reference=alignment.template.dat, taxonomy=tax.taxonomy.dat, method=knn, numwanted=10, search=blast, match=1, mismatch=-1, gapopen=-2, gapextend=-1, relabund=false, printlevel=-1, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | ./mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:03:54.993513", "params": {"count": "null", "name": "null", "relabund": "\"false\"", "tax": "{\"source2\": \"hist\", \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 305}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\"", "classify": "{\"search\": {\"algorithm\": \"blast\", \"gapopen\": \"-2\", \"mismatch\": \"-1\", \"__current_case__\": 1, \"gapextend\": \"-1\", \"match\": \"1\"}, \"numwanted\": \"10\", \"method\": \"knn\", \"__current_case__\": 1}", "printlevel": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "alignment": "{\"source\": \"hist\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 304}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n./mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "10403", "id": "00c35829965cb81b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"taxonomy": {"src": "hda", "id": "466b5293998bb5d6"}, "tree": {"src": "hda", "id": "906904e43ca63ecd"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "466b5293998bb5d6", "uuid": "f20e3c76-1740-4eff-8630-3d567e7839be"}, "tree": {"src": "hda", "id": "906904e43ca63ecd", "uuid": "4af15274-31d4-47f9-8d4c-b4e4f9a9adcf"}}, "update_time": "2018-02-08T17:04:27.158188", "tool_id": "mothur_classify_tree", "outputs": {"out_tree": {"src": "hda", "id": "1eb4a85cdfd1d969", "uuid": "104fa8be-7644-42c1-ac6a-5d57cf6fbe19"}, "logfile": {"src": "hda", "id": "59d26e2d28c3eb74", "uuid": "4320b983-e868-4c16-87da-966b2e111b80"}, "summary": {"src": "hda", "id": "8078f99fccaa607a", "uuid": "6b82ae77-a2de-422f-9cc5-652ce31296b1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > classify.tree(tree=tree.dat,taxonomy=taxonomy.dat)\na is not in your taxonomy file.  I will not include it in the consensus.\nd is not in your taxonomy file.  I will not include it in the consensus.\na is not in your taxonomy file.  I will not include it in the consensus.\nd is not in your taxonomy file.  I will not include it in the consensus.\nf is not in your taxonomy file.  I will not include it in the consensus.\n\n\nIt took 0 secs to find the concensus taxonomies.\n\nOutput File Names: \ntree.taxonomy.summary\ntree.taxonomy.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_311.dat' tree.dat && ln -s 'None' name.dat && ln -s 'None' group.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_310.dat' taxonomy.dat &&  echo 'classify.tree( tree=tree.dat, taxonomy=taxonomy.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:04:23.889464", "params": {"cutoff": "\"51\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\"", "group": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "11070", "id": "1fb9c7b21f94ef77", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_classify_tree.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input|source": "phylip", "input|infile": {"src": "hda", "id": "e71a1c7a27ae6506"}}, "job": {"inputs": {"infile": {"src": "hda", "id": "e71a1c7a27ae6506", "uuid": "eb16f0aa-2f7d-4385-a0d9-8893849c19bc"}}, "update_time": "2018-02-08T17:04:49.595673", "tool_id": "mothur_clearcut", "outputs": {"logfile": {"src": "hda", "id": "b41e07faea40178d", "uuid": "17ef5d40-149c-43ad-a520-f7546721c4cf"}, "tree": {"src": "hda", "id": "0ea0054cb0d7ae96", "uuid": "ab2586c0-c483-47ff-98ce-5c92766ad47b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > clearcut(phylip=input.infile.dat,ntrees=1,norandom=false,shuffle=false, \rexpblen=OFF,expdist=OFF,neighbor=true)\n\nOutput File Names: \ninput.infile.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_315.dat' input.infile.dat &&  echo 'clearcut( phylip=input.infile.dat, ntrees=1, norandom=false, shuffle=false, expblen=OFF, expdist=OFF, neighbor=true )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:04:46.486175", "params": {"expdist": "\"false\"", "ntrees": "\"1\"", "shuffle": "\"false\"", "matrixout": "\"false\"", "dbkey": "\"hg17\"", "norandom": "\"false\"", "seed": "\"\"", "expblen": "\"false\"", "neighbor": "\"true\"", "input": "{\"source\": \"phylip\", \"infile\": {\"values\": [{\"src\": \"hda\", \"id\": 315}]}, \"__current_case__\": 2}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "11169", "id": "cf18f77993464b22", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_clearcut.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"expdist": true, "ntrees": "3", "shuffle": true, "norandom": true, "input|infile": {"src": "hda", "id": "aa70baf734620bdc"}, "matrixout": true, "input|source": "phylip", "expblen": true, "neighbor": false}, "job": {"inputs": {"infile": {"src": "hda", "id": "aa70baf734620bdc", "uuid": "c5ef22fd-857f-4977-a690-b821788054f9"}}, "update_time": "2018-02-08T17:05:03.113363", "tool_id": "mothur_clearcut", "outputs": {"logfile": {"src": "hda", "id": "2b0e2d16a6440935", "uuid": "c487b0c3-d332-43b8-be67-8ac767c93ab2"}, "tree": {"src": "hda", "id": "a81292b81d01663f", "uuid": "e5ce56a6-79c4-47d5-83b8-6cc4a6f68013"}, "matrix": {"src": "hda", "id": "e6bde25d0e72014d", "uuid": "09b640a1-dc3a-4ce9-ba5e-451e328abf99"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > clearcut(phylip=input.infile.dat,matrixout=matrixout.dist,ntrees=3,nora \rndom=true,shuffle=true,expblen=ON,expdist=ON,neighbor=false)\n\nOutput File Names: \ninput.infile.tre\nmatrixout.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_318.dat' input.infile.dat &&  echo 'clearcut( phylip=input.infile.dat, matrixout=matrixout.dist, ntrees=3, norandom=true, shuffle=true, expblen=ON, expdist=ON, neighbor=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:04:59.020694", "params": {"expdist": "\"true\"", "ntrees": "\"3\"", "shuffle": "\"true\"", "matrixout": "\"true\"", "dbkey": "\"hg17\"", "norandom": "\"true\"", "seed": "\"\"", "expblen": "\"true\"", "neighbor": "\"false\"", "input": "{\"source\": \"phylip\", \"infile\": {\"values\": [{\"src\": \"hda\", \"id\": 318}]}, \"__current_case__\": 2}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "11257", "id": "161ef5576377f4a0", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_clearcut.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"matrixout": true, "input|source": "dna", "input|infile": {"src": "hda", "id": "3b972a2e0d2ad508"}}, "job": {"inputs": {"infile": {"src": "hda", "id": "3b972a2e0d2ad508", "uuid": "42b137e8-ee9a-4fcd-9125-f44f25e16653"}}, "update_time": "2018-02-08T17:05:23.706458", "tool_id": "mothur_clearcut", "outputs": {"logfile": {"src": "hda", "id": "bf269ecfb1e2517b", "uuid": "f08be317-84d0-40a3-9e7f-71c6f8c47ebf"}, "tree": {"src": "hda", "id": "b756dc95aa3bca1d", "uuid": "29b63329-68d2-466e-8cbc-4f2bb9822b12"}, "matrix": {"src": "hda", "id": "72392165690065e0", "uuid": "94005b9d-5213-43f1-8ed6-624f86aa72d1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > clearcut(fasta=input.infile.dat,DNA=true,matrixout=matrixout.dist,ntree \rs=1,norandom=false,shuffle=false,expblen=OFF,expdist=OFF,neighbor=true)\n\nOutput File Names: \ninput.infile.tre\nmatrixout.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_322.dat' input.infile.dat &&  echo 'clearcut( fasta=input.infile.dat, DNA=true, matrixout=matrixout.dist, ntrees=1, norandom=false, shuffle=false, expblen=OFF, expdist=OFF, neighbor=true )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:05:20.414063", "params": {"expdist": "\"false\"", "ntrees": "\"1\"", "shuffle": "\"false\"", "matrixout": "\"true\"", "dbkey": "\"hg17\"", "norandom": "\"false\"", "seed": "\"\"", "expblen": "\"false\"", "neighbor": "\"true\"", "input": "{\"source\": \"dna\", \"infile\": {\"values\": [{\"src\": \"hda\", \"id\": 322}]}, \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "11345", "id": "f21e60058e4146e2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_clearcut.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"matrix|format": "phylip", "matrix|dist": {"src": "hda", "id": "94bd5fbd2d4dc748"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "94bd5fbd2d4dc748", "uuid": "ad044749-8a81-439a-9fc9-cef9c22d1dcc"}}, "update_time": "2018-02-08T17:05:42.437919", "tool_id": "mothur_cluster", "outputs": {"rabund": {"src": "hda", "id": "35e639f464fb8f4d", "uuid": "1d4871ed-9f54-483f-95fd-5ec6e68af090"}, "logfile": {"src": "hda", "id": "ffc368cd972b6cba", "uuid": "309c09e9-25e7-4587-aa9b-610dbfed4648"}, "otulist": {"src": "hda", "id": "3c43ce8ab3a9cd20", "uuid": "a2c686bc-bc70-4ece-af0b-387a4e03ba6d"}, "sabund": {"src": "hda", "id": "475e4ad0b99b0c18", "uuid": "53f99ebc-3088-43cc-9403-64b6b285ba67"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster(phylip=matrix.dist.dat,metric=mcc,initialize=singleton,delta=0. \r0001,iters=100,precision=100,sim=false,method=opti)\n\nUsing 1 processors.\n\nYou did not set a cutoff, using 0.03.\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering matrix.dist.dat\n\n\niter\ttime\tlabel\tnum_otus\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t0\t0.03\t98\t0.03\t0\t4736\t0\t17\t0\t1\t0\t0.996423\t0\t0.996423\t0\t0\t\n1\t0\t0.03\t88\t0.03\t17\t4736\t0\t0\t1\t1\t1\t1\t0\t1\t1\t1\t\n2\t0\t0.03\t88\t0.03\t17\t4736\t0\t0\t1\t1\t1\t1\t0\t1\t1\t1\t\n\n\nIt took 0 seconds to cluster\n\nOutput File Names: \nmatrix.dist.opti_mcc.list\nmatrix.dist.opti_mcc.steps\nmatrix.dist.opti_mcc.sabund\nmatrix.dist.opti_mcc.rabund\nmatrix.dist.opti_mcc.sensspec\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_326.dat' matrix.dist.dat && ln -s 'None' matrix.name.dat && ln -s 'None' count.dat &&  echo 'cluster( phylip=matrix.dist.dat, metric=mcc, initialize=singleton, delta=0.0001, iters=100, precision=100, sim=false, method=opti )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:05:37.908897", "params": {"count": "null", "cutoff": "\"0.0\"", "matrix": "{\"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 326}]}, \"name\": null, \"__current_case__\": 1, \"format\": \"phylip\"}", "select_method": "{\"iters\": \"100\", \"metric\": \"mcc\", \"__current_case__\": 5, \"delta\": \"0.0001\", \"initialize\": \"singleton\", \"method\": \"opti\"}", "dbkey": "\"hg17\"", "precision": "\"100\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "sim": "\"false\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "11445", "id": "c95281174db2641a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"matrix|format": "column", "matrix|dist": {"src": "hda", "id": "555065f5aff402d2"}, "matrix|name": {"src": "hda", "id": "597e4b92c7768991"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "555065f5aff402d2", "uuid": "a8c89c54-a556-4e5a-bffc-3a38dd6130d8"}, "name": {"src": "hda", "id": "597e4b92c7768991", "uuid": "5f592839-3c46-4865-9ccc-734ebdc5e415"}}, "update_time": "2018-02-08T17:06:18.213444", "tool_id": "mothur_cluster", "outputs": {"rabund": {"src": "hda", "id": "ea74846895a98ad3", "uuid": "aa327386-1426-45e7-9f55-12e85d15b4ec"}, "logfile": {"src": "hda", "id": "6a9009e6b944272b", "uuid": "bfad486b-574e-4864-9770-3aadc0bf5a3f"}, "otulist": {"src": "hda", "id": "90fd946e89881eaf", "uuid": "d1317f90-e5ab-4c75-8679-28965c9824ae"}, "sabund": {"src": "hda", "id": "2df305d2bcf63841", "uuid": "b0c4d1d2-56c8-47cc-a5a0-cb68bca73f8b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster(column=matrix.dist.dat,name=matrix.name.dat,metric=mcc,initiali \rze=singleton,delta=0.0001,iters=100,precision=100,sim=false,method=opti)\n\nUsing 1 processors.\n\nYou did not set a cutoff, using 0.03.\n\nClustering matrix.dist.dat\n\n\niter\ttime\tlabel\tnum_otus\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t0\t0.03\t96\t0.03\t0\t4560\t0\t0\t0\t1\t0\t1\t0\t1\t0\t0\t\n1\t0\t0.03\t96\t0.03\t0\t4560\t0\t0\t0\t1\t0\t1\t0\t1\t0\t0\t\n\n\nIt took 0 seconds to cluster\n\nOutput File Names: \nmatrix.dist.opti_mcc.list\nmatrix.dist.opti_mcc.steps\nmatrix.dist.opti_mcc.sabund\nmatrix.dist.opti_mcc.rabund\nmatrix.dist.opti_mcc.sensspec\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_331.dat' matrix.dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_332.dat' matrix.name.dat && ln -s 'None' count.dat &&  echo 'cluster( column=matrix.dist.dat, name=matrix.name.dat, metric=mcc, initialize=singleton, delta=0.0001, iters=100, precision=100, sim=false, method=opti )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:06:12.756285", "params": {"count": "null", "cutoff": "\"0.0\"", "matrix": "{\"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 331}]}, \"name\": {\"values\": [{\"src\": \"hda\", \"id\": 332}]}, \"__current_case__\": 0, \"format\": \"column\"}", "select_method": "{\"iters\": \"100\", \"metric\": \"mcc\", \"__current_case__\": 5, \"delta\": \"0.0001\", \"initialize\": \"singleton\", \"method\": \"opti\"}", "dbkey": "\"hg17\"", "precision": "\"100\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "sim": "\"false\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "11596", "id": "26b7e36460fca86e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"matrix|format": "column", "matrix|dist": {"src": "hda", "id": "8ea35917f4649fec"}, "matrix|name": {"src": "hda", "id": "48c17343dcb0fe59"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "8ea35917f4649fec", "uuid": "c9f7d113-9030-4115-82ee-9d65edd27e3a"}, "name": {"src": "hda", "id": "48c17343dcb0fe59", "uuid": "4174a4bd-d31b-42e3-9a07-b5858c5b925a"}}, "update_time": "2018-02-08T17:06:51.168891", "tool_id": "mothur_cluster", "outputs": {"rabund": {"src": "hda", "id": "459ebd1d4b9be0d2", "uuid": "c8f134ea-eb5e-4118-9fbb-57397b54ef29"}, "logfile": {"src": "hda", "id": "940151f28ccfd679", "uuid": "3ce4b4ef-c34d-43af-8595-156fea1810ec"}, "otulist": {"src": "hda", "id": "acb5efb55c8f2fca", "uuid": "b9eed437-fa24-4763-9798-48ebc331434d"}, "sabund": {"src": "hda", "id": "86fc1a32b14d4612", "uuid": "97a259d7-58c2-4e3e-9301-9f6b4eaf1012"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster(column=matrix.dist.dat,name=matrix.name.dat,metric=mcc,initiali \rze=singleton,delta=0.0001,iters=100,precision=100,sim=false,method=opti)\n\nUsing 1 processors.\n\nYou did not set a cutoff, using 0.03.\n\nClustering matrix.dist.dat\n\n\niter\ttime\tlabel\tnum_otus\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t0\t0.03\t96\t0.03\t0\t4560\t0\t0\t0\t1\t0\t1\t0\t1\t0\t0\t\n1\t0\t0.03\t96\t0.03\t0\t4560\t0\t0\t0\t1\t0\t1\t0\t1\t0\t0\t\n\n\nIt took 0 seconds to cluster\n\nOutput File Names: \nmatrix.dist.opti_mcc.list\nmatrix.dist.opti_mcc.steps\nmatrix.dist.opti_mcc.sabund\nmatrix.dist.opti_mcc.rabund\nmatrix.dist.opti_mcc.sensspec\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_337.dat' matrix.dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_338.dat' matrix.name.dat && ln -s 'None' count.dat &&  echo 'cluster( column=matrix.dist.dat, name=matrix.name.dat, metric=mcc, initialize=singleton, delta=0.0001, iters=100, precision=100, sim=false, method=opti )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:06:46.589877", "params": {"count": "null", "cutoff": "\"0.0\"", "matrix": "{\"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 337}]}, \"name\": {\"values\": [{\"src\": \"hda\", \"id\": 338}]}, \"__current_case__\": 0, \"format\": \"column\"}", "select_method": "{\"iters\": \"100\", \"metric\": \"mcc\", \"__current_case__\": 5, \"delta\": \"0.0001\", \"initialize\": \"singleton\", \"method\": \"opti\"}", "dbkey": "\"hg17\"", "precision": "\"100\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "sim": "\"false\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "11767", "id": "5c14fa19c3fe9aa2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"dist": {"src": "hda", "id": "c2096fa94981c9cc"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "c2096fa94981c9cc", "uuid": "457e36fb-13ec-40ee-9969-e08fefad8496"}}, "update_time": "2018-02-08T17:07:21.690682", "tool_id": "mothur_cluster_classic", "outputs": {"rabund": {"src": "hda", "id": "aa6cc630da5109fb", "uuid": "564a1502-1ffc-414c-91dd-bb7b7a442616"}, "logfile": {"src": "hda", "id": "37f9ab3378d23774", "uuid": "69ef929f-cc25-41b2-86a0-2d58b70bf44e"}, "otulist": {"src": "hda", "id": "4c469a959b869c08", "uuid": "8e7894e4-13ae-4ba0-a182-db5048ef9f4d"}, "sabund": {"src": "hda", "id": "8c559fb88d75a36b", "uuid": "e2b7d2e7-d821-4291-8384-da431189328d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > cluster.classic(phylip=dist.dat,method=average,precision=100,sim=false) \r\u001b[A\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[K)\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\nunique\t1\t24\n1.75\t2\t22\t1\n2.01\t2\t20\t2\n2.10\t2\t18\t3\n2.13\t2\t16\t4\n2.22\t2\t14\t5\n2.26\t3\t11\t5\t1\n2.42\t5\t11\t4\t0\t0\t1\n2.93\t6\t10\t4\t0\t0\t0\t1\n3.07\t6\t10\t2\t0\t1\t0\t1\n3.27\t6\t9\t1\t1\t1\t0\t1\n3.34\t6\t7\t2\t1\t1\t0\t1\n3.44\t6\t6\t1\t2\t1\t0\t1\n3.53\t7\t6\t1\t1\t0\t0\t1\t1\n3.56\t7\t4\t2\t1\t0\t0\t1\t1\n4.07\t7\t3\t2\t0\t1\t0\t1\t1\n4.15\t13\t3\t2\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t1\n4.58\t13\t2\t1\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t1\n4.72\t13\t1\t1\t1\t0\t1\t0\t0\t0\t0\t0\t0\t0\t1\n5.18\t16\t1\t1\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\n5.76\t21\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\n5.91\t23\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\n6.67\t24\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\n\nOutput File Names: \ndist.an.sabund\ndist.an.rabund\ndist.an.list\n\nIt took 0 seconds to cluster\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_343.dat' dist.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'cluster.classic( phylip=dist.dat, method=average, precision=100, sim=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:07:18.320079", "params": {"count": "null", "cutoff": "\"\"", "name": "null", "precision": "\"100\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"average\"", "sim": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "11897", "id": "fc5c2ad70cbb4f9f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_classic.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "82ea1c58d22fbeef"}, "names": {"src": "hda", "id": "3d5f803521123c6e"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "82ea1c58d22fbeef", "uuid": "4b29d8b2-b22d-4643-a7f1-7bdb8254276e"}, "names": {"src": "hda", "id": "3d5f803521123c6e", "uuid": "342207f4-9855-4fa3-ab02-b062f576deb6"}}, "update_time": "2018-02-08T17:07:53.344919", "tool_id": "mothur_cluster_fragments", "outputs": {"out_names": {"src": "hda", "id": "0c1eec7a0b69039e", "uuid": "397fead2-7a43-4716-8db4-a1f09b18b77a"}, "logfile": {"src": "hda", "id": "d5273cf5fa0c242d", "uuid": "a5fa27a5-b40b-4bcb-8cd9-e909b56c9370"}, "out_fasta": {"src": "hda", "id": "ec0fb831200675f4", "uuid": "db083fe2-064f-4445-837c-2584ba3c2999"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > cluster.fragments(fasta=fasta.dat,diffs=0,percent=0,name=names.dat)\n0\t98\t0\n98\t96\t2\n\nTotal number of sequences before cluster.fragments was 98.\ncluster.fragments removed 2 sequences.\n\nIt took 0 secs to cluster 98 sequences.\n\nOutput File Names: \nfasta.fragclust.fasta\nfasta.fragclust.names\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_348.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_349.dat' names.dat && ln -s 'None' count.dat &&  echo 'cluster.fragments( fasta=fasta.dat, diffs=0, percent=0, name=names.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:07:49.188733", "params": {"count": "null", "diffs": "\"0\"", "percent": "\"0\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "12010", "id": "83e248eabb1b3d31", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_fragments.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby|condmethod|method": "average", "splitby|matrix|format": "phylip", "splitby|matrix|dist": {"src": "hda", "id": "f1f75462f416e186"}, "splitby|splitmethod": "distance"}, "job": {"inputs": {"splitby|dist": {"src": "hda", "id": "f1f75462f416e186", "uuid": "74f96c23-ef2d-4632-abaa-2b2a0d763fab"}}, "update_time": "2018-02-08T17:08:20.393794", "tool_id": "mothur_cluster_split", "outputs": {"rabund": {"src": "hda", "id": "f283e96027016ec6", "uuid": "d18af698-5952-4a8f-aae0-9daddd004626"}, "logfile": {"src": "hda", "id": "0ab9f8045882e86f", "uuid": "a832c53d-dbd3-4455-85f3-1bf23af63e6e"}, "otulist": {"src": "hda", "id": "2c72ab2ea314d830", "uuid": "c2874287-ffa4-4064-b4bb-e682011a03b9"}, "sabund": {"src": "hda", "id": "f3e7443ed4070d7c", "uuid": "b1621de1-03a0-4536-81db-30c4948b7a8f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=distance,phylip=splitby.matrix.dist.dat,metho \rd=average,precision=100,large=false,cluster=true,runsensspec=true,processors=1)\n\nUsing 1 processors.\nConverting to column format...\nIt took 0 seconds to convert the distance file.\nSplitting the file...\nIt took 0 seconds to split the distance file.\n\nReading splitby.matrix.dist.column.dist.2.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.matrix.dist.column.dist.2.temp\nCutoff was 0.15 changed cutoff to 0.11\n\nReading splitby.matrix.dist.column.dist.5.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.matrix.dist.column.dist.5.temp\nCutoff was 0.15 changed cutoff to 0.14\n\nReading splitby.matrix.dist.column.dist.1.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.matrix.dist.column.dist.1.temp\n\nReading splitby.matrix.dist.column.dist.7.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.matrix.dist.column.dist.7.temp\nCutoff was 0.15 changed cutoff to 0.12\n\nReading splitby.matrix.dist.column.dist.4.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.matrix.dist.column.dist.4.temp\nCutoff was 0.15 changed cutoff to 0.13\n\nReading splitby.matrix.dist.column.dist.6.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.matrix.dist.column.dist.6.temp\n\nReading splitby.matrix.dist.column.dist.3.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.matrix.dist.column.dist.3.temp\n\nReading splitby.matrix.dist.column.dist.10.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.matrix.dist.column.dist.10.temp\n\nReading splitby.matrix.dist.column.dist.13.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.matrix.dist.column.dist.13.temp\n\nReading splitby.matrix.dist.column.dist.0.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.matrix.dist.column.dist.0.temp\n\nReading splitby.matrix.dist.column.dist.9.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.matrix.dist.column.dist.9.temp\n\nReading splitby.matrix.dist.column.dist.11.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.matrix.dist.column.dist.11.temp\n\nReading splitby.matrix.dist.column.dist.12.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.matrix.dist.column.dist.12.temp\n\nCutoff was 0.15 changed cutoff to 0.11\nIt took 0 seconds to cluster\nMerging the clustered files...\nIt took 0 seconds to merge.\n\nOutput File Names: \nsplitby.matrix.dist.column.an.sabund\nsplitby.matrix.dist.column.an.rabund\nsplitby.matrix.dist.column.an.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_353.dat' splitby.matrix.dist.dat && ln -s 'None' splitby.matrix.nameOrCount.dat &&  echo 'cluster.split( splitmethod=distance, phylip=splitby.matrix.dist.dat, method=average, precision=100, large=false, cluster=true, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:08:15.820483", "params": {"runsensspec": "\"true\"", "cutoff": "\"0.0\"", "splitby": "{\"splitmethod\": \"distance\", \"condmethod\": {\"method\": \"average\", \"__current_case__\": 2}, \"matrix\": {\"nameOrCount\": null, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 353}]}, \"__current_case__\": 1, \"format\": \"phylip\"}, \"__current_case__\": 0}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "12104", "id": "4e27b888e0f89616", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby|condmethod|method": "average", "cluster": false, "splitby|matrix|format": "phylip", "splitby|matrix|dist": {"src": "hda", "id": "22ac87488bc814b9"}, "splitby|splitmethod": "distance"}, "job": {"inputs": {"splitby|dist": {"src": "hda", "id": "22ac87488bc814b9", "uuid": "c5ddd9c1-e9b1-4dc8-b471-62e1cbe7a970"}}, "update_time": "2018-02-08T17:08:54.553537", "tool_id": "mothur_cluster_split", "outputs": {"__new_primary_file_9|7__": {"src": "hda", "id": "6cc323ea174af743", "uuid": "8d26ad52-9bce-4d0f-a128-b83232d63c1f"}, "__new_primary_file_9|13__": {"src": "hda", "id": "09f8fd3b2e41755d", "uuid": "9dfe2404-8d7d-4c8f-9a12-e4ab0f96348f"}, "__new_primary_file_extra|9__": {"src": "hda", "id": "4b964545b41f57a8", "uuid": "9c3fb19a-ae9a-483d-ae59-748b4fbba575"}, "__new_primary_file_extra|13__": {"src": "hda", "id": "f85178165ba80947", "uuid": "d9eb5cc4-dc67-4594-b6de-f1124b2fd87a"}, "splitfile": {"src": "hda", "id": "2b49763c55874680", "uuid": "a2e63b7f-b705-4c61-b529-35a803f011b6"}, "__new_primary_file_9|6__": {"src": "hda", "id": "158be0d01c91f0d3", "uuid": "bbffb137-e152-482f-9ace-f67324722714"}, "__new_primary_file_extra|12__": {"src": "hda", "id": "721a73f13e9921b7", "uuid": "f81f533a-0778-4f91-9207-e4c6d719af46"}, "__new_primary_file_9|4__": {"src": "hda", "id": "709f4e85f6d2c262", "uuid": "becf4ab3-c26a-486c-ab10-33b3825c8df7"}, "__new_primary_file_9|9__": {"src": "hda", "id": "64b146a0a237cf0e", "uuid": "febc9484-9717-44ff-af5d-45b9754a6fc1"}, "__new_primary_file_extra|1__": {"src": "hda", "id": "0aed0175215b082a", "uuid": "ea0c11c9-c633-4875-949c-f09c41bc174e"}, "__new_primary_file_9|10__": {"src": "hda", "id": "a5b8d21ac8fc30ea", "uuid": "68d1b13a-2f52-448c-a2e9-c2afce62a48e"}, "otulist": {"src": "hda", "id": "9b8f9fbdb2c6dd2c", "uuid": "c14e1520-e196-4f6c-8ba7-e7aeeeb304bf"}, "rabund": {"src": "hda", "id": "25296282d079fac6", "uuid": "a86dcd47-c38c-459d-931f-ae8bcc85f6f4"}, "__new_primary_file_9|1__": {"src": "hda", "id": "18d19b643e7062cc", "uuid": "54c1d879-b21a-4847-aed7-99baa3d0dd33"}, "__new_primary_file_extra|2__": {"src": "hda", "id": "943b175492f370d8", "uuid": "492e9178-cdd8-4980-a515-c5b5893c190d"}, "__new_primary_file_extra|4__": {"src": "hda", "id": "4b36d8f744e89cdc", "uuid": "2b557902-ec34-4d1e-9ffd-6684b6cb6aaa"}, "__new_primary_file_extra|3__": {"src": "hda", "id": "f2c720655bd71813", "uuid": "aa9544d9-d154-4660-91d1-2e1148f4d3d8"}, "__new_primary_file_9|3__": {"src": "hda", "id": "ec3c9d08d9062ead", "uuid": "9011b542-a9ce-4969-a7db-03335616cc9f"}, "logfile": {"src": "hda", "id": "a5170ff908b4401b", "uuid": "a2151d9c-8c36-4d47-9aad-6de7c3cc8c28"}, "__new_primary_file_extra|5__": {"src": "hda", "id": "3b057c0454a7c801", "uuid": "a3af2bdb-7aa7-41a3-be3b-2fe53ea22060"}, "__new_primary_file_9|2__": {"src": "hda", "id": "759c19e61550929d", "uuid": "ba70dc4a-4d0f-4520-b7d6-fb30b0537e73"}, "__new_primary_file_9|11__": {"src": "hda", "id": "43766c028675eda0", "uuid": "89a4c048-b087-4bdd-b710-824f099129b2"}, "__new_primary_file_extra|6__": {"src": "hda", "id": "07fd1c8ec8f13176", "uuid": "664abf4a-5daa-4332-a09f-e855aa50d616"}, "sabund": {"src": "hda", "id": "c1fc90e177f46aff", "uuid": "03d7e66e-b2d6-44ec-a951-085714c44993"}, "__new_primary_file_extra|7__": {"src": "hda", "id": "5adbd2172c54d7c8", "uuid": "edba9c0a-9a76-4763-ad86-9e5dce81155c"}, "__new_primary_file_9|5__": {"src": "hda", "id": "802ffc5c50268813", "uuid": "5e40989a-9e9d-4a19-86f7-817b94d331da"}, "__new_primary_file_extra|11__": {"src": "hda", "id": "20b89408decf8a23", "uuid": "ef137ee7-ea8d-4b59-85f1-dd5e2dc31c27"}, "__new_primary_file_9|0__": {"src": "hda", "id": "d49ecd190d765ffa", "uuid": "19c3dc84-9217-4b1e-89c7-a39d84bcaa66"}, "__new_primary_file_extra|extra__": {"src": "hda", "id": "2915b60ef025819a", "uuid": "ed8f847c-6e65-4458-9167-55265ad85dbb"}, "__new_primary_file_extra|0__": {"src": "hda", "id": "af2b33d2c4a65f6c", "uuid": "623ad805-121d-4e8d-ae7d-5a5cd9dddb10"}, "__new_primary_file_extra|10__": {"src": "hda", "id": "3c8273a46e218a3f", "uuid": "2a5dbc9d-f71c-411b-bb5f-7f403f708199"}, "__new_primary_file_9|12__": {"src": "hda", "id": "84069f8e0a4c5a8e", "uuid": "5a41226d-54e2-41f6-9058-be37cfb62bd5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=distance,phylip=splitby.matrix.dist.dat,metho \rd=average,precision=100,large=false,cluster=false,runsensspec=true,processors=1) \r\u001b[A\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[K)\n\nUsing 1 processors.\nConverting to column format...\nIt took 0 seconds to convert the distance file.\nSplitting the file...\nIt took 0 seconds to split the distance file.\n\nOutput File Names: \n\nsplitby.matrix.dist.column.file\nsplitby.matrix.dist.column.dist.2.temp\nsplitby.matrix.dist.dat.names.2.temp\nsplitby.matrix.dist.column.dist.5.temp\nsplitby.matrix.dist.dat.names.5.temp\nsplitby.matrix.dist.column.dist.1.temp\nsplitby.matrix.dist.dat.names.1.temp\nsplitby.matrix.dist.column.dist.7.temp\nsplitby.matrix.dist.dat.names.7.temp\nsplitby.matrix.dist.column.dist.4.temp\nsplitby.matrix.dist.dat.names.4.temp\nsplitby.matrix.dist.column.dist.6.temp\nsplitby.matrix.dist.dat.names.6.temp\nsplitby.matrix.dist.column.dist.3.temp\nsplitby.matrix.dist.dat.names.3.temp\nsplitby.matrix.dist.column.dist.10.temp\nsplitby.matrix.dist.dat.names.10.temp\nsplitby.matrix.dist.column.dist.13.temp\nsplitby.matrix.dist.dat.names.13.temp\nsplitby.matrix.dist.column.dist.0.temp\nsplitby.matrix.dist.dat.names.0.temp\nsplitby.matrix.dist.column.dist.9.temp\nsplitby.matrix.dist.dat.names.9.temp\nsplitby.matrix.dist.column.dist.11.temp\nsplitby.matrix.dist.dat.names.11.temp\nsplitby.matrix.dist.column.dist.12.temp\nsplitby.matrix.dist.dat.names.12.temp\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_358.dat' splitby.matrix.dist.dat && ln -s 'None' splitby.matrix.nameOrCount.dat &&  echo 'cluster.split( splitmethod=distance, phylip=splitby.matrix.dist.dat, method=average, precision=100, large=false, cluster=false, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:08:47.634172", "params": {"runsensspec": "\"true\"", "cutoff": "\"0.0\"", "splitby": "{\"splitmethod\": \"distance\", \"condmethod\": {\"method\": \"average\", \"__current_case__\": 2}, \"matrix\": {\"nameOrCount\": null, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 358}]}, \"__current_case__\": 1, \"format\": \"phylip\"}, \"__current_case__\": 0}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "12239", "id": "d760e1d92679b730", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby|taxonomy": {"src": "hda", "id": "0af7797da2f1a1c7"}, "splitby|condmethod|method": "average", "splitby|splitmethod": "classify", "splitby|dist": {"src": "hda", "id": "732b43bd12cd060f"}, "splitby|nameOrCount": {"src": "hda", "id": "b7d5085eacaa6509"}}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "b7d5085eacaa6509", "uuid": "f3ee5a09-1ec0-4b77-b0ef-9a3dafda896d"}, "taxonomy": {"src": "hda", "id": "0af7797da2f1a1c7", "uuid": "61860e61-15bb-4d6a-9de7-b1c9df4cf18e"}, "dist": {"src": "hda", "id": "732b43bd12cd060f", "uuid": "f4a7c395-0387-4a9b-8653-dc3131dc8eb0"}}, "update_time": "2018-02-08T17:09:37.257438", "tool_id": "mothur_cluster_split", "outputs": {"rabund": {"src": "hda", "id": "fde5d0b73a42236a", "uuid": "8732d6da-19a3-40bd-86a8-9500089d5048"}, "logfile": {"src": "hda", "id": "de19e90a144e923c", "uuid": "45df5879-94af-48ac-b35e-df3cd6caafc9"}, "otulist": {"src": "hda", "id": "6ed393d03ba7fd0e", "uuid": "846f0381-4cbb-4aa2-bd67-1c2482726beb"}, "sabund": {"src": "hda", "id": "7535296d23a37c60", "uuid": "2baef149-c8d7-455d-9460-07edf376752b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=classify,column=splitby.dist.dat,taxonomy=spl \ritby.taxonomy.dat,name=splitby.nameOrCount.dat,taxlevel=1,method=average,precisi \ron=100,large=false,cluster=true,runsensspec=true,processors=1)\n\nUsing 1 processors.\nSplitting the file...\nIt took 0 seconds to split the distance file.\n\nReading splitby.dist.dat.0.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.dist.dat.0.temp\nIt took 0 seconds to cluster\nMerging the clustered files...\nIt took 0 seconds to merge.\n\nOutput File Names: \nsplitby.dist.an.sabund\nsplitby.dist.an.rabund\nsplitby.dist.an.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_391.dat' splitby.dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_393.dat' splitby.nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_392.dat' splitby.taxonomy.dat &&  echo 'cluster.split( splitmethod=classify, column=splitby.dist.dat, taxonomy=splitby.taxonomy.dat, name=splitby.nameOrCount.dat, taxlevel=1, method=average, precision=100, large=false, cluster=true, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:09:31.700719", "params": {"runsensspec": "\"true\"", "cutoff": "\"0.0\"", "splitby": "{\"splitmethod\": \"classify\", \"condmethod\": {\"method\": \"average\", \"__current_case__\": 2}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 391}]}, \"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 393}]}, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 392}]}, \"__current_case__\": 1, \"taxlevel\": \"1\"}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "12408", "id": "449eb427f528cea7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby|taxonomy": {"src": "hda", "id": "957dec9f2200cbe4"}, "splitby|condmethod|method": "average", "splitby|splitmethod": "classify", "splitby|dist": {"src": "hda", "id": "fcbedabdda23c338"}, "splitby|nameOrCount": {"src": "hda", "id": "7f45e41d747c3b22"}}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "7f45e41d747c3b22", "uuid": "495ee28e-4f96-447e-9d34-8388522ce56d"}, "taxonomy": {"src": "hda", "id": "957dec9f2200cbe4", "uuid": "0e1582f5-cba2-44fc-9afd-a6a6a68bcf12"}, "dist": {"src": "hda", "id": "fcbedabdda23c338", "uuid": "16c9486e-d67a-4e27-a72f-8f18dfd26971"}}, "update_time": "2018-02-08T17:10:13.687017", "tool_id": "mothur_cluster_split", "outputs": {"logfile": {"src": "hda", "id": "a6780727682706fd", "uuid": "ebe106d6-2ee0-47b6-9d24-4fd6e52e36fb"}, "otulist": {"src": "hda", "id": "c809b2abaed97358", "uuid": "f5f10b68-5385-4a18-97b8-7bd03cd541d8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=classify,column=splitby.dist.dat,taxonomy=spl \ritby.taxonomy.dat,count=splitby.nameOrCount.dat,taxlevel=1,method=average,precis \rion=100,large=false,cluster=true,runsensspec=true,processors=1)\n\nUsing 1 processors.\nSplitting the file...\nIt took 0 seconds to split the distance file.\n\nReading splitby.dist.dat.0.temp\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.dist.dat.0.temp\nIt took 0 seconds to cluster\nMerging the clustered files...\nIt took 0 seconds to merge.\n\nOutput File Names: \nsplitby.dist.an.unique_list.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_398.dat' splitby.dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_400.dat' splitby.nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_399.dat' splitby.taxonomy.dat &&  echo 'cluster.split( splitmethod=classify, column=splitby.dist.dat, taxonomy=splitby.taxonomy.dat, count=splitby.nameOrCount.dat, taxlevel=1, method=average, precision=100, large=false, cluster=true, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:10:09.362326", "params": {"runsensspec": "\"true\"", "cutoff": "\"0.0\"", "splitby": "{\"splitmethod\": \"classify\", \"condmethod\": {\"method\": \"average\", \"__current_case__\": 2}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 398}]}, \"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 400}]}, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 399}]}, \"__current_case__\": 1, \"taxlevel\": \"1\"}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "12591", "id": "8bfda5654e551614", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby|taxonomy": {"src": "hda", "id": "6fb516af7370ea7a"}, "splitby|fasta": {"src": "hda", "id": "71bc98c5ef351f59"}, "splitby|condmethod|method": "average", "cutoff": "9999", "splitby|splitmethod": "fasta", "splitby|nameOrCount": {"src": "hda", "id": "63f8201b30d2cadd"}}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "63f8201b30d2cadd", "uuid": "ced19938-b32a-477b-9b2f-7f97faff871f"}, "taxonomy": {"src": "hda", "id": "6fb516af7370ea7a", "uuid": "cea8d185-870c-488d-84eb-544d8084b763"}, "fasta": {"src": "hda", "id": "71bc98c5ef351f59", "uuid": "107d7fcb-2c10-4ee1-91ca-285b91ceafe6"}}, "update_time": "2018-02-08T17:10:41.676918", "tool_id": "mothur_cluster_split", "outputs": {"rabund": {"src": "hda", "id": "41a728572c331a9d", "uuid": "91789c46-7cc2-46b9-b081-8a8330db86b1"}, "logfile": {"src": "hda", "id": "dfb58ec7c7cde5ba", "uuid": "709949a8-e538-4f95-b9fd-3cfdcb6aeca9"}, "otulist": {"src": "hda", "id": "598476a21fa893cd", "uuid": "bc4b64e8-3ad1-4287-9e78-6ea4bad03d30"}, "sabund": {"src": "hda", "id": "9c8aa3de76c5f0c4", "uuid": "8cc44192-61ab-4e70-a827-b3f559379040"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=fasta,fasta=splitby.fasta.dat,taxonomy=splitb \ry.taxonomy.dat,name=splitby.nameOrCount.dat,taxlevel=3,classic=false,method=aver \rage,cutoff=9999.0,precision=100,large=false,cluster=true,runsensspec=true,proces \rsors=1)\n\nUsing 1 processors.\nSplitting the file...\n/******************************************/\nRunning command: dist.seqs(fasta=splitby.fasta.dat.0.temp, processors=1, cutoff=9999)\n\nUsing 1 processors.\n/******************************************/\n0\t0\n1\t0\n\nOutput File Names: \nsplitby.fasta.dat.0.dist\n\nIt took 0 seconds to calculate the distances for 2 sequences.\nIt took 0 seconds to split the distance file.\n\nReading splitby.fasta.dat.0.dist\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nClustering splitby.fasta.dat.0.dist\nIt took 0 seconds to cluster\nMerging the clustered files...\nIt took 0 seconds to merge.\n\nOutput File Names: \nsplitby.fasta.an.sabund\nsplitby.fasta.an.rabund\nsplitby.fasta.an.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_403.dat' splitby.fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_405.dat' splitby.nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_404.dat' splitby.taxonomy.dat &&  echo 'cluster.split( splitmethod=fasta, fasta=splitby.fasta.dat, taxonomy=splitby.taxonomy.dat, name=splitby.nameOrCount.dat, taxlevel=3, classic=false, method=average, cutoff=9999.0, precision=100, large=false, cluster=true, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:10:36.383791", "params": {"runsensspec": "\"true\"", "cutoff": "\"9999.0\"", "splitby": "{\"splitmethod\": \"fasta\", \"condmethod\": {\"method\": \"average\", \"__current_case__\": 2}, \"classic\": \"false\", \"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 405}]}, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 404}]}, \"__current_case__\": 2, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 403}]}, \"taxlevel\": \"3\"}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "12771", "id": "c48fc7b200585e1b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby|taxonomy": {"src": "hda", "id": "3529226cbbc41f8d"}, "splitby|fasta": {"src": "hda", "id": "f8fb2d243923edf0"}, "splitby|condmethod|method": "agc", "splitby|splitmethod": "fasta", "splitby|nameOrCount": {"src": "hda", "id": "77d4412f77f6b180"}}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "77d4412f77f6b180", "uuid": "e91d0fcc-18a6-4a8a-8a57-d58f08d5d4af"}, "taxonomy": {"src": "hda", "id": "3529226cbbc41f8d", "uuid": "07076206-9095-48f8-9629-8ad06d34a2f9"}, "fasta": {"src": "hda", "id": "f8fb2d243923edf0", "uuid": "73a485b3-aa97-46b3-aba3-2badac802195"}}, "update_time": "2018-02-08T17:11:20.597824", "tool_id": "mothur_cluster_split", "outputs": {"rabund": {"src": "hda", "id": "c397987c596ee46a", "uuid": "6f652e8d-9dbb-4c3b-9c9b-95182510e58d"}, "logfile": {"src": "hda", "id": "7196b214b6870b7e", "uuid": "0ae1803c-9339-41a6-91f4-53e28da0bb6d"}, "otulist": {"src": "hda", "id": "94d7eab7ff1b5670", "uuid": "90d83bd3-0e54-4b4b-9d24-3c0e6339bf4c"}, "sabund": {"src": "hda", "id": "d5962eb1211503b9", "uuid": "b6587fd2-8292-457a-9b9a-e4f8b659d078"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=fasta,fasta=splitby.fasta.dat,taxonomy=splitb \ry.taxonomy.dat,name=splitby.nameOrCount.dat,taxlevel=3,classic=false,method=agc, \rprecision=100,large=false,cluster=true,runsensspec=true,processors=1)\n\nUsing 1 processors.\nSplitting the file...\n\nYou did not set a cutoff, using 0.03.\n/home/saskia/miniconda3/envs/mulled-v1-736475004b65901caa33ce32368de7bd390f9f20eaf8369d7ccbbf0be4fb73c4/bin/mothurvsearch file does not exist. Checking path... \nFound vsearch in your path, using /home/saskia/miniconda3/envs/mulled-v1-736475004b65901caa33ce32368de7bd390f9f20eaf8369d7ccbbf0be4fb73c4/bin/vsearch\nIt took 0 seconds to split the distance file.\n\nClustering splitby.fasta.dat.0.temp\nIt took 0 seconds to cluster\nMerging the clustered files...\nIt took 0 seconds to merge.\n\nOutput File Names: \nsplitby.fasta.agc.sabund\nsplitby.fasta.agc.rabund\nsplitby.fasta.agc.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_410.dat' splitby.fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_412.dat' splitby.nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_411.dat' splitby.taxonomy.dat &&  echo 'cluster.split( splitmethod=fasta, fasta=splitby.fasta.dat, taxonomy=splitby.taxonomy.dat, name=splitby.nameOrCount.dat, taxlevel=3, classic=false, method=agc, precision=100, large=false, cluster=true, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:11:15.331832", "params": {"runsensspec": "\"true\"", "cutoff": "\"0.0\"", "splitby": "{\"splitmethod\": \"fasta\", \"condmethod\": {\"method\": \"agc\", \"__current_case__\": 3}, \"classic\": \"false\", \"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 412}]}, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 411}]}, \"__current_case__\": 2, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 410}]}, \"taxlevel\": \"3\"}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "vsearch v2.6.0_linux_x86_64, 62.8GB RAM, 8 cores\nhttps://github.com/torognes/vsearch\n\nReading file splitby.fasta.dat.0.temp.sorted.fasta.temp 100%\n1873 nt in 2 seqs, min 930, max 943, avg 936\nMasking 100%\nCounting k-mers 100%\nClustering 100%\nSorting clusters 100%\nWriting clusters 100%\nClusters: 2 Size min 1, max 1, avg 1.0\nSingletons: 2, 100.0% of seqs, 100.0% of clusters\n", "job_metrics": [], "model_class": "Job", "external_id": "12940", "id": "3af8c7b9f683116f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000005", "has_data": true}, {"data": {"status": "success", "inputs": {"splitby|condmethod|method": "opti", "splitby|matrix|format": "phylip", "splitby|matrix|dist": {"src": "hda", "id": "f5edea7d52e42cd6"}, "splitby|splitmethod": "distance"}, "job": {"inputs": {"splitby|dist": {"src": "hda", "id": "f5edea7d52e42cd6", "uuid": "59e654f0-8e3f-40f2-a48d-7cb6cc2360f3"}}, "update_time": "2018-02-08T17:11:50.352932", "tool_id": "mothur_cluster_split", "outputs": {"rabund": {"src": "hda", "id": "69ae44680e47ff1d", "uuid": "90e27f2b-c64d-41c8-b138-04ab9781c74f"}, "sensspec": {"src": "hda", "id": "9fa13b46d25f1a47", "uuid": "ee1e6cc4-52ab-418d-aa6e-d5338c6319f3"}, "logfile": {"src": "hda", "id": "2be21af3e0b30a72", "uuid": "a41387cc-7003-4dc9-9946-85e75f38884b"}, "otulist": {"src": "hda", "id": "8f5442c8ae200d3a", "uuid": "3c429842-3285-4b6e-9296-2ed6722d7f27"}, "sabund": {"src": "hda", "id": "e6b222c9649e44d2", "uuid": "8c096a41-2fd1-4857-af5f-7d4ce21cef45"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\u001b[?1034h\nmothur > cluster.split(splitmethod=distance,phylip=splitby.matrix.dist.dat,metho \rd=opti,metric=mcc,initialize=singleton,delta=0.0001,iters=100,precision=100,larg \re=false,cluster=true,runsensspec=true,processors=1)\n\nUsing 1 processors.\nConverting to column format...\nIt took 0 seconds to convert the distance file.\nSplitting the file...\nIt took 0 seconds to split the distance file.\n\nYou did not set a cutoff, using 0.03.\n\nClustering splitby.matrix.dist.column.dist.2.temp\n\ntp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t3735\t0\t6\t0\t1\t0\t0.998396\t0\t0.998396\t0\t0\t\n\n\nYou did not set a cutoff, using 0.03.\n\nClustering splitby.matrix.dist.column.dist.0.temp\n\ntp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t3735\t0\t6\t0\t1\t0\t0.998396\t0\t0.998396\t0\t0\t\n\n\nYou did not set a cutoff, using 0.03.\n\nClustering splitby.matrix.dist.column.dist.3.temp\n\ntp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t3652\t0\t3\t0\t1\t0\t0.999179\t0\t0.999179\t0\t0\t\n\n\nYou did not set a cutoff, using 0.03.\n\nClustering splitby.matrix.dist.column.dist.1.temp\n\ntp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t3569\t0\t1\t0\t1\t0\t0.99972\t0\t0.99972\t0\t0\t\n\n\nYou did not set a cutoff, using 0.03.\n\nClustering splitby.matrix.dist.column.dist.4.temp\n\ntp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0\t3569\t0\t1\t0\t1\t0\t0.99972\t0\t0.99972\t0\t0\t\n\nIt took 0 seconds to cluster\nMerging the clustered files...\nIt took 0 seconds to merge.\n/******************************************/\nRunning command: sens.spec(cutoff=0.03, list=splitby.matrix.dist.column.opti_mcc.list, phylip=splitby.matrix.dist.dat, name=splitby.matrix.dist.dat.names)\n\nNOTE: sens.spec assumes that only unique sequences were used to generate the distance matrix.\n\n0.03\nIt took 0 to run sens.spec.\n\nOutput File Names: \nsplitby.matrix.dist.column.opti_mcc.sensspec\n\n/******************************************/\nDone.\n\n\nlabel\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n0.03\t0.03\t0\t4736\t0\t17\t0\t1\t0\t0.9964\t0\t0.9964\t0\t0\n\nOutput File Names: \nsplitby.matrix.dist.column.opti_mcc.sabund\nsplitby.matrix.dist.column.opti_mcc.rabund\nsplitby.matrix.dist.column.opti_mcc.list\nsplitby.matrix.dist.column.opti_mcc.sensspec\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_417.dat' splitby.matrix.dist.dat && ln -s 'None' splitby.matrix.nameOrCount.dat &&  echo 'cluster.split( splitmethod=distance, phylip=splitby.matrix.dist.dat, method=opti, metric=mcc, initialize=singleton, delta=0.0001, iters=100, precision=100, large=false, cluster=true, runsensspec=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:11:45.894758", "params": {"runsensspec": "\"true\"", "cutoff": "\"0.0\"", "splitby": "{\"splitmethod\": \"distance\", \"condmethod\": {\"iters\": \"100\", \"metric\": \"mcc\", \"__current_case__\": 3, \"delta\": \"0.0001\", \"initialize\": \"singleton\", \"method\": \"opti\"}, \"matrix\": {\"nameOrCount\": null, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 417}]}, \"__current_case__\": 1, \"format\": \"phylip\"}, \"__current_case__\": 0}", "precision": "\"100\"", "dbkey": "\"hg17\"", "large": "\"false\"", "cluster": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "13078", "id": "b7d4a98a7bb9e1bc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cluster_split.test_tool_000006", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "6eb09fe0ca80e9ad"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "6eb09fe0ca80e9ad", "uuid": "d2d740da-4498-40f5-b809-01cb26b7e829"}}, "update_time": "2018-02-08T17:12:25.413981", "tool_id": "mothur_collect_shared", "outputs": {"__new_primary_file_thetayc|jabund__": {"src": "hda", "id": "09dbeac489d85549", "uuid": "d9c1ae28-881d-4501-85d5-33667b47309f"}, "__new_primary_file_thetayc|jest__": {"src": "hda", "id": "3a07e8fa101f66c3", "uuid": "3aa67a68-55bc-49be-970a-065c3e3f022b"}, "__new_primary_file_thetayc|sorclass__": {"src": "hda", "id": "457390d412d4922c", "uuid": "a9107de5-1ffa-412d-ab9a-c2b6f14ead9f"}, "__new_primary_file_thetayc|thetayc__": {"src": "hda", "id": "6c12052addbdbf10", "uuid": "99933db3-30b7-4f45-b0ca-e4e3cc1da9ee"}, "__new_primary_file_thetayc|sorabund__": {"src": "hda", "id": "7b32cfe10869d24e", "uuid": "7fa144d9-5695-473c-83a5-341fa500b861"}, "__new_primary_file_thetayc|shared.chao__": {"src": "hda", "id": "a8b7bad9a0464ba9", "uuid": "849e6208-1c61-4b1e-b3e2-4f29352f74bd"}, "__new_primary_file_thetayc|sorest__": {"src": "hda", "id": "3fc9b5ca07992501", "uuid": "34314ff0-2518-43f0-b5dc-d1129b3ad0fc"}, "__new_primary_file_thetayc|shared.sobs__": {"src": "hda", "id": "5f49ccb40e6bf114", "uuid": "7db453f9-365a-4cba-b0ec-97f034dd5d49"}, "__new_primary_file_thetayc|thetan__": {"src": "hda", "id": "2cfb598380799c5c", "uuid": "35caf54a-a243-4695-80a1-377ce870793a"}, "logfile": {"src": "hda", "id": "41fcf23659876b66", "uuid": "9c77450f-0cb7-4dac-baaa-ff4336aa23ed"}, "__new_primary_file_thetayc|jclass__": {"src": "hda", "id": "43c7ced58110ff4d", "uuid": "0d2d47c8-e779-425c-ad2f-cfa734b53eff"}, "__new_primary_file_thetayc|shared.ace__": {"src": "hda", "id": "07efabe7adaf6e12", "uuid": "cea5d499-2702-4f2f-9405-3d70e3d681a1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > collect.shared(shared=otu.dat,calc=sharedsobs-sharedchao-sharedace-jcla \rss-jest-sorclass-sorest-jabund-sorabund-thetan-thetayc,freq=100.0,all=true)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.shared.sobs\notu.shared.chao\notu.shared.ace\notu.jclass\notu.jest\notu.sorclass\notu.sorest\notu.jabund\notu.sorabund\notu.thetan\notu.thetayc\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_423.dat' otu.dat &&  echo 'collect.shared( shared=otu.dat, calc=sharedsobs-sharedchao-sharedace-jclass-jest-sorclass-sorest-jabund-sorabund-thetan-thetayc, freq=100.0, all=true )' | sed 's/ //g' | mothur | tee mothur.out.log && rm otu.dat", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:12:21.966900", "params": {"dbkey": "\"hg17\"", "label": "null", "groups": "null", "freq": "\"100.0\"", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"jclass\", \"jest\", \"sorclass\", \"sorest\", \"jabund\", \"sorabund\", \"thetan\", \"thetayc\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13205", "id": "8984b162f62c6c24", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_collect_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"calc": ["sharedsobs", "sharedchao", "sharedace", "anderberg", "jclass", "jest", "kulczynski", "kulczynskicody", "kstest", "lennon", "ochiai", "sorclass", "sorest", "whittaker", "hamming", "memchi2", "memchord", "memeuclidean", "mempearson", "braycurtis", "jabund", "morisitahorn", "sorabund", "thetan", "thetayc", "canberra", "gower", "hellinger", "manhattan", "odum", "soergel", "spearman", "speciesprofile", "structchi2", "structchord", "structeuclidean", "structkulczynski", "structpearson", "sharednseqs"], "otu": {"src": "hda", "id": "3e47ebdf403a2dd1"}, "groups": ["forest", "pasture"], "label": ["0.03", "0.05", "0.22"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "3e47ebdf403a2dd1", "uuid": "c4207529-1bc3-44b7-9110-967e843f2544"}}, "update_time": "2018-02-08T17:12:45.362338", "tool_id": "mothur_collect_shared", "outputs": {"__new_primary_file_whittaker|mempearson__": {"src": "hda", "id": "2b215f192af96e2f", "uuid": "cecc2250-db1a-4c37-9d24-d73c011d1abc"}, "__new_primary_file_whittaker|manhattan__": {"src": "hda", "id": "07fd9a413201852e", "uuid": "d70a8e27-c95d-4554-a285-459f0e18354c"}, "__new_primary_file_whittaker|gower__": {"src": "hda", "id": "fd1e10e0f0d76fac", "uuid": "03420e9a-6924-4dc9-a224-b72db0e5558a"}, "__new_primary_file_whittaker|structpearson__": {"src": "hda", "id": "82d89e614ebda5c1", "uuid": "51ab641a-5e2e-40a9-88e8-e8037d9f1e6a"}, "__new_primary_file_whittaker|thetayc__": {"src": "hda", "id": "3df0a01a3ae34d52", "uuid": "546e7e77-f2c3-49f5-a1a0-014e2f5f400c"}, "__new_primary_file_whittaker|sorclass__": {"src": "hda", "id": "0d63eb5c811d9a5b", "uuid": "e1c6c74f-2af8-436e-ad8c-b688e7791215"}, "__new_primary_file_whittaker|whittaker__": {"src": "hda", "id": "fc6a9ef5f7630e87", "uuid": "7b5512d4-aa1f-48bf-bc5a-295406139240"}, "__new_primary_file_whittaker|hellinger__": {"src": "hda", "id": "78fdca853d645da8", "uuid": "c9c7c063-bdea-4576-9c17-707aa732667e"}, "__new_primary_file_whittaker|lennon__": {"src": "hda", "id": "eb492223fe45a3a1", "uuid": "55ecafe7-fdc9-4d09-821a-69a7bea023fa"}, "__new_primary_file_whittaker|anderberg__": {"src": "hda", "id": "f7cac463734b28ae", "uuid": "010a3fd5-5254-4d09-8562-fa3f38c26ae0"}, "__new_primary_file_whittaker|hamming__": {"src": "hda", "id": "032dc790b013bafc", "uuid": "4a8d06b3-ac49-431f-a96c-932e23af81c9"}, "__new_primary_file_whittaker|shared.sobs__": {"src": "hda", "id": "c9e276c91d77be76", "uuid": "5eeba6a8-f91f-491a-95ad-00b655abba36"}, "__new_primary_file_whittaker|sorabund__": {"src": "hda", "id": "cf6f5650773911ff", "uuid": "45d9148b-2992-46cf-ae88-a4024e68acd2"}, "__new_primary_file_whittaker|speciesprofile__": {"src": "hda", "id": "dd09e5318fcac9cd", "uuid": "21ec4299-981e-472f-9ee4-1af55871c4a4"}, "__new_primary_file_whittaker|structchi2__": {"src": "hda", "id": "cc61617d359bbeb4", "uuid": "98e5435d-ab04-4c9c-a8ef-bbcf8a0b396b"}, "__new_primary_file_whittaker|jest__": {"src": "hda", "id": "06134b0ededad71e", "uuid": "083dbc1c-3adb-4333-aac5-fc487c02b14b"}, "__new_primary_file_whittaker|thetan__": {"src": "hda", "id": "ace828d96e9bc93f", "uuid": "85aa130c-ed1d-4bc6-b4ae-bab5a4229910"}, "__new_primary_file_whittaker|shared.chao__": {"src": "hda", "id": "d27681472e68c286", "uuid": "d22d8971-fb37-4dab-a896-3c16da9cd88d"}, "__new_primary_file_whittaker|morisitahorn__": {"src": "hda", "id": "89eb04d15155113e", "uuid": "c5a36a03-64be-44d8-a3b1-9ac4042bc8ae"}, "__new_primary_file_whittaker|memchi2__": {"src": "hda", "id": "c70fd0f87d1321b9", "uuid": "cccbdcb1-95ea-4b3e-a01e-4389fe29dcf1"}, "__new_primary_file_whittaker|jclass__": {"src": "hda", "id": "4a03c449ab1f345a", "uuid": "7b7910a3-a461-4a15-97b6-0b6b5b0028dd"}, "__new_primary_file_whittaker|structeuclidean__": {"src": "hda", "id": "64eba53a47060775", "uuid": "0d3b86ba-b129-40f6-b7a7-17c6df06a266"}, "__new_primary_file_whittaker|structkulczynski__": {"src": "hda", "id": "8617c587cd9e4e77", "uuid": "b69d8972-f8c4-44ae-80f8-fbcd73a74e0f"}, "__new_primary_file_whittaker|memeuclidean__": {"src": "hda", "id": "5c48130196180838", "uuid": "5654d852-104b-46d4-b850-ba523b238c7f"}, "__new_primary_file_whittaker|structchord__": {"src": "hda", "id": "7206901401158c4a", "uuid": "677b89a0-54b2-43f5-96f8-df5422cea5ff"}, "__new_primary_file_whittaker|ochiai__": {"src": "hda", "id": "c9ef78ff932a2539", "uuid": "69a341de-3ccc-4e20-94b4-eead506e8d14"}, "__new_primary_file_whittaker|braycurtis__": {"src": "hda", "id": "3cb3ad12c0574547", "uuid": "cec9891f-dbec-40d8-bc6a-63c99c85f3d0"}, "__new_primary_file_whittaker|canberra__": {"src": "hda", "id": "010d772e12940e81", "uuid": "c484d80a-c5da-4b7d-b280-a49020407453"}, "__new_primary_file_whittaker|shared.nseqs__": {"src": "hda", "id": "11fff4f70c354168", "uuid": "66154bc9-063b-4970-b223-8f4734d31bf6"}, "logfile": {"src": "hda", "id": "36f33e00653500e8", "uuid": "25e5fc6d-b192-48f2-9a37-98afbb5e8744"}, "__new_primary_file_whittaker|memchord__": {"src": "hda", "id": "5c0379f640540f7d", "uuid": "12c00f31-5beb-4d47-89f8-2bc512ed9336"}, "__new_primary_file_whittaker|kulczynskicody__": {"src": "hda", "id": "0a0eeda241196907", "uuid": "41b900b0-e92e-4bd6-a8b9-6162181f6f3f"}, "__new_primary_file_whittaker|spearman__": {"src": "hda", "id": "6e055b0f6b730971", "uuid": "54ad0a10-a404-48f7-aeb8-1c0c12137878"}, "__new_primary_file_whittaker|shared.ace__": {"src": "hda", "id": "864ad45f69d33ad2", "uuid": "c34a956f-7b6d-44ac-abcd-13568970b2bf"}, "__new_primary_file_whittaker|soergel__": {"src": "hda", "id": "7536865915d87753", "uuid": "6f387274-a14a-4ade-ac1c-22d001bdf696"}, "__new_primary_file_whittaker|odum__": {"src": "hda", "id": "ab313dd72b645b75", "uuid": "a7ad4d37-2d02-4eb8-99fa-c6ff83f4ccf8"}, "__new_primary_file_whittaker|kstest__": {"src": "hda", "id": "446f6e70c8f6f247", "uuid": "4bdc0101-cb98-43a5-b4be-8673e035ca1d"}, "__new_primary_file_whittaker|sorest__": {"src": "hda", "id": "b8252606b6759e88", "uuid": "9577bc6a-357f-4bc0-8d49-c141496fd520"}, "__new_primary_file_whittaker|jabund__": {"src": "hda", "id": "a12cdd35a80cbdf3", "uuid": "f3c84a67-78c1-4581-8e51-e270e5baa92b"}, "__new_primary_file_whittaker|kulczynski__": {"src": "hda", "id": "2afa7a4578b8f4fd", "uuid": "18326c68-5ed7-49eb-9fe9-f1e23139b73a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > collect.shared(shared=otu.dat,label=0.03-0.05-0.22,calc=sharedsobs-shar \redchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-kstest-lennon-o \rchiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-memeuclidean-mempearson \r-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-canberra-gower-hellinger \r-manhattan-odum-soergel-spearman-speciesprofile-structchi2-structchord-structeuc \rlidean-structkulczynski-structpearson-sharednseqs,groups=forest-pasture,freq=100 \r.0,all=true)\n0.03\n0.05\n0.22\n\nOutput File Names: \notu.shared.sobs\notu.shared.chao\notu.shared.ace\notu.anderberg\notu.jclass\notu.jest\notu.kulczynski\notu.kulczynskicody\notu.kstest\notu.lennon\notu.ochiai\notu.sorclass\notu.sorest\notu.whittaker\notu.hamming\notu.memchi2\notu.memchord\notu.memeuclidean\notu.mempearson\notu.braycurtis\notu.jabund\notu.morisitahorn\notu.sorabund\notu.thetan\notu.thetayc\notu.canberra\notu.gower\notu.hellinger\notu.manhattan\notu.odum\notu.soergel\notu.spearman\notu.speciesprofile\notu.structchi2\notu.structchord\notu.structeuclidean\notu.structkulczynski\notu.structpearson\notu.shared.nseqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_436.dat' otu.dat &&  echo 'collect.shared( shared=otu.dat, label=0.03-0.05-0.22, calc=sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-kstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-memeuclidean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-canberra-gower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-structchi2-structchord-structeuclidean-structkulczynski-structpearson-sharednseqs, groups=forest-pasture, freq=100.0, all=true )' | sed 's/ //g' | mothur | tee mothur.out.log && rm otu.dat", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:12:40.316603", "params": {"dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.22\"]", "groups": "[\"forest\", \"pasture\"]", "freq": "\"100.0\"", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"anderberg\", \"jclass\", \"jest\", \"kulczynski\", \"kulczynskicody\", \"kstest\", \"lennon\", \"ochiai\", \"sorclass\", \"sorest\", \"whittaker\", \"hamming\", \"memchi2\", \"memchord\", \"memeuclidean\", \"mempearson\", \"braycurtis\", \"jabund\", \"morisitahorn\", \"sorabund\", \"thetan\", \"thetayc\", \"canberra\", \"gower\", \"hellinger\", \"manhattan\", \"odum\", \"soergel\", \"spearman\", \"speciesprofile\", \"structchi2\", \"structchord\", \"structeuclidean\", \"structkulczynski\", \"structpearson\", \"sharednseqs\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13306", "id": "71db30c33f7a1d97", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_collect_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "77c3626ab0594697"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "77c3626ab0594697", "uuid": "b215e272-d061-4228-b42c-f2ceb82e2668"}}, "update_time": "2018-02-08T17:13:04.454824", "tool_id": "mothur_collect_single", "outputs": {"__new_primary_file_sobs|ace__": {"src": "hda", "id": "191434f645ec622f", "uuid": "027519e4-1115-40a8-b787-fef65bb75865"}, "__new_primary_file_sobs|shannon__": {"src": "hda", "id": "9ee2e00a0d8ff0c1", "uuid": "db8e108e-cd33-4eb1-8889-a7214a6da043"}, "__new_primary_file_sobs|sobs__": {"src": "hda", "id": "f060dd6bec0b0c91", "uuid": "9aa5224d-5d1a-47b8-825a-a0ebdf95c615"}, "__new_primary_file_sobs|chao__": {"src": "hda", "id": "dd28ab0e62f6c657", "uuid": "6cc80384-1ab4-45fd-9747-33db889e16d8"}, "__new_primary_file_sobs|jack__": {"src": "hda", "id": "982b968aefffd7e6", "uuid": "ece0b874-fdca-4647-b5f0-340b0c38aa54"}, "__new_primary_file_sobs|npshannon__": {"src": "hda", "id": "4dfde39352bb574f", "uuid": "e53eda85-f247-4cfa-a1be-f1a80608d29f"}, "logfile": {"src": "hda", "id": "50eb45139d0d6a93", "uuid": "113d9767-5ec5-441d-8a41-ed74b6095e1b"}, "__new_primary_file_sobs|simpson__": {"src": "hda", "id": "2e7d279ca3333738", "uuid": "53f30268-939b-4087-9e34-adcd6250a341"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > collect.single(list=otu.dat,calc=ace-chao-jack-sobs-simpson-shannon-nps \rhannon,abund=10,freq=100.0)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.ace\notu.chao\notu.jack\notu.sobs\notu.simpson\notu.shannon\notu.npshannon\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_477.dat' otu.dat &&  echo 'collect.single( list=otu.dat, calc=ace-chao-jack-sobs-simpson-shannon-npshannon, abund=10, freq=100.0 )' | sed 's/ //g' | mothur | tee mothur.out.log && rm otu.dat", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:13:00.966122", "params": {"abund": "\"10\"", "dbkey": "\"hg17\"", "label": "null", "freq": "\"100.0\"", "calc": "[\"ace\", \"chao\", \"jack\", \"sobs\", \"simpson\", \"shannon\", \"npshannon\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13392", "id": "c6239e5379f31f0f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_collect_single.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"calc": ["ace", "bootstrap", "chao", "jack", "sobs", "simpsoneven", "shannoneven", "heip", "smithwilson", "bergerparker", "coverage", "goodscoverage", "simpson", "invsimpson", "qstat", "shannon", "npshannon", "boneh", "efron", "shen", "solow", "logseries", "geometric", "bstick", "nseqs"], "otu": {"src": "hda", "id": "599aa42a6f638c3c"}, "label": ["0.36", "0.38", "0.41"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "599aa42a6f638c3c", "uuid": "0933dde9-2f47-471a-a6d3-abec09250959"}}, "update_time": "2018-02-08T17:13:26.296010", "tool_id": "mothur_collect_single", "outputs": {"__new_primary_file_solow|simpson__": {"src": "hda", "id": "ddfa564d1c57beab", "uuid": "75ff5504-acd1-40aa-9031-5097db7dd66b"}, "__new_primary_file_solow|simpsoneven__": {"src": "hda", "id": "3808e741d551ae79", "uuid": "deb08319-362f-4c01-a945-2cce9b31fbc8"}, "__new_primary_file_solow|chao__": {"src": "hda", "id": "4c17a0c0b24f3d2a", "uuid": "62ed1247-d5d3-402f-af91-87380a3b9a17"}, "__new_primary_file_solow|sobs__": {"src": "hda", "id": "bd9ebfe83c09a924", "uuid": "2ee19aa2-3b9b-4e4c-a3f2-1ceb4fc294dc"}, "__new_primary_file_solow|bootstrap__": {"src": "hda", "id": "c33192ec797333a8", "uuid": "a7124b13-6151-4e62-a30a-59f6e1efd035"}, "__new_primary_file_solow|logseries__": {"src": "hda", "id": "30389f7c5465c626", "uuid": "d72c0749-4314-4300-9965-cb8ccec89074"}, "__new_primary_file_solow|ace__": {"src": "hda", "id": "d13b0aeade1f3b9f", "uuid": "9100a533-4087-4376-80dc-9892685d7a8b"}, "__new_primary_file_solow|shen__": {"src": "hda", "id": "b0746254f283297c", "uuid": "d6ef866c-0e64-4db7-8899-b45492e2cb44"}, "__new_primary_file_solow|shannoneven__": {"src": "hda", "id": "5300091d026f85af", "uuid": "088ccdc7-fd4d-4506-8531-2353c772eaa4"}, "__new_primary_file_solow|invsimpson__": {"src": "hda", "id": "b3c2b8853f254e86", "uuid": "72cefb8a-92dc-406f-8ea8-0478f9c8baf3"}, "__new_primary_file_solow|jack__": {"src": "hda", "id": "5932136d963c1318", "uuid": "af006a66-4002-4656-b6c7-1b5c105e8851"}, "__new_primary_file_solow|smithwilson__": {"src": "hda", "id": "de3955fb86630a7e", "uuid": "cb2307ab-a198-48e6-a9ee-93d01df34577"}, "__new_primary_file_solow|boneh__": {"src": "hda", "id": "98cd146bafa9f05e", "uuid": "e42d3b64-8117-4b4f-9930-e7ea9ce7d3d0"}, "__new_primary_file_solow|heip__": {"src": "hda", "id": "7a298366c9388d2f", "uuid": "81e2119b-a66b-4ff1-9796-90458fdc87bd"}, "__new_primary_file_solow|geometric__": {"src": "hda", "id": "2c905c266975a822", "uuid": "19e08439-6a2d-45e3-884e-ad716a4bdb6b"}, "__new_primary_file_solow|shannon__": {"src": "hda", "id": "9bebc27cdf46e887", "uuid": "9fc5a622-8063-41bb-8926-262d0bbe7a37"}, "__new_primary_file_solow|bergerparker__": {"src": "hda", "id": "a8a72597d313e674", "uuid": "6de9fb48-8aed-441e-9732-7ea6008adb0b"}, "__new_primary_file_solow|coverage__": {"src": "hda", "id": "5989b468f72bfcf5", "uuid": "5ddbac9d-e350-4d10-b2d0-b71c34a9da9f"}, "__new_primary_file_solow|npshannon__": {"src": "hda", "id": "3307079e08296ced", "uuid": "0c946a77-8e44-44a9-bb6d-b3b81b9c4d63"}, "__new_primary_file_solow|qstat__": {"src": "hda", "id": "bdfaaa58b77537a7", "uuid": "69617fe1-149e-4f11-952b-d2ffeb16d878"}, "logfile": {"src": "hda", "id": "480b3d56ed97c000", "uuid": "47827789-b03e-43e5-a90f-a3572067b330"}, "__new_primary_file_solow|goodscoverage__": {"src": "hda", "id": "d8859fda823215ee", "uuid": "069b6dc7-a02b-42d6-bf83-e8b5a99d8b83"}, "__new_primary_file_solow|nseqs__": {"src": "hda", "id": "b7c449f860774475", "uuid": "ab61d3db-886d-434c-9f90-b7e17ef7951c"}, "__new_primary_file_solow|bstick__": {"src": "hda", "id": "b0c02b917db38b13", "uuid": "1a591dcb-9e93-4488-afcb-7d14e6acb6ba"}, "__new_primary_file_solow|solow__": {"src": "hda", "id": "3679dac861a4e053", "uuid": "9d5f072d-49c9-413d-a968-364281350165"}, "__new_primary_file_solow|efron__": {"src": "hda", "id": "37b49f3ca84157b5", "uuid": "41d7ec1e-3b60-4640-ba13-dd2405473bea"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > collect.single(sabund=otu.dat,label=0.36-0.38-0.41,calc=ace-bootstrap-c \rhao-jack-sobs-simpsoneven-shannoneven-heip-smithwilson-bergerparker-coverage-goo \rdscoverage-simpson-invsimpson-qstat-shannon-npshannon-boneh-efron-shen-solow-log \rseries-geometric-bstick-nseqs,abund=10,freq=100.0)\n0.36\n0.38\n0.41\n\nOutput File Names: \notu.ace\notu.bootstrap\notu.chao\notu.jack\notu.sobs\notu.simpsoneven\notu.shannoneven\notu.heip\notu.smithwilson\notu.bergerparker\notu.coverage\notu.goodscoverage\notu.simpson\notu.invsimpson\notu.qstat\notu.shannon\notu.npshannon\notu.boneh\notu.efron\notu.shen\notu.solow\notu.logseries\notu.geometric\notu.bstick\notu.nseqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_486.dat' otu.dat &&  echo 'collect.single( sabund=otu.dat, label=0.36-0.38-0.41, calc=ace-bootstrap-chao-jack-sobs-simpsoneven-shannoneven-heip-smithwilson-bergerparker-coverage-goodscoverage-simpson-invsimpson-qstat-shannon-npshannon-boneh-efron-shen-solow-logseries-geometric-bstick-nseqs, abund=10, freq=100.0 )' | sed 's/ //g' | mothur | tee mothur.out.log && rm otu.dat", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:13:22.030750", "params": {"abund": "\"10\"", "dbkey": "\"hg17\"", "label": "[\"0.36\", \"0.38\", \"0.41\"]", "freq": "\"100.0\"", "calc": "[\"ace\", \"bootstrap\", \"chao\", \"jack\", \"sobs\", \"simpsoneven\", \"shannoneven\", \"heip\", \"smithwilson\", \"bergerparker\", \"coverage\", \"goodscoverage\", \"simpson\", \"invsimpson\", \"qstat\", \"shannon\", \"npshannon\", \"boneh\", \"efron\", \"shen\", \"solow\", \"logseries\", \"geometric\", \"bstick\", \"nseqs\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13485", "id": "cd5f25030bbf4788", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_collect_single.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "966d85c09a3ba224"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "966d85c09a3ba224", "uuid": "4e106005-f312-4492-9215-949aa781008a"}}, "update_time": "2018-02-08T17:13:46.721790", "tool_id": "mothur_consensus_seqs", "outputs": {"logfile": {"src": "hda", "id": "7dabb5bd245b7e86", "uuid": "3be51f90-2742-4388-a1ab-2fefa8ee76d8"}, "cons_fasta": {"src": "hda", "id": "e4b28fee36db3ded", "uuid": "f4dee734-7be1-4e34-82aa-6186612713aa"}, "summary": {"src": "hda", "id": "499ab5633737b2d3", "uuid": "213fe84b-bf79-40b9-9b5a-3e504993a354"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > consensus.seqs(fasta=fasta.dat)\nIt took 0 secs to find the consensus sequences.\nOutput File Names: \nfasta.cons.summary\nfasta.cons.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_513.dat' fasta.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'consensus.seqs( fasta=fasta.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:13:42.630431", "params": {"count": "null", "cutoff": "\"\"", "name": "null", "dbkey": "\"hg17\"", "perotu": "{\"use\": \"no\", \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13578", "id": "33d716567e7a5529", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_consensus_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "83dfe49f50126b60"}, "perotu|otu": {"src": "hda", "id": "93ee5b88b9257311"}, "fasta": {"src": "hda", "id": "ed149d1c3c9443b2"}, "perotu|use": "yes"}, "job": {"inputs": {"count": {"src": "hda", "id": "83dfe49f50126b60", "uuid": "3620f06b-5ed4-4d25-8e52-d35f73c0e498"}, "fasta": {"src": "hda", "id": "ed149d1c3c9443b2", "uuid": "dadc920c-ef1b-476d-a7ad-c9abca0a2882"}, "otu": {"src": "hda", "id": "93ee5b88b9257311", "uuid": "e3746a8a-8017-4045-a09c-eb7e45d10277"}}, "update_time": "2018-02-08T17:14:23.581097", "tool_id": "mothur_consensus_seqs", "outputs": {"__new_primary_file_unique|0.30__": {"src": "hda", "id": "c9376b9862484ed4", "uuid": "1e9d5969-e4a9-4f38-b87f-401e7ca8b6c9"}, "logfile": {"src": "hda", "id": "6d049149a6f947d3", "uuid": "cb42d6d1-fa4d-4359-bb3b-0e99648b5f8d"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "a15361ef356dda4c", "uuid": "3abca939-41b6-4841-8cb9-2bdc41db1d6d"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "270b3503788ebdd6", "uuid": "160db0d3-3bb6-4f56-84c5-d915cf2ff6b0"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > consensus.seqs(fasta=fasta.dat,list=perotu.otu.dat,count=count.dat)\nunique\n0.30\n0.33\nIt took 1 secs to find the consensus sequences.\nOutput File Names: \nfasta.unique.cons.summary\nfasta.unique.cons.names\nfasta.unique.cons.fasta\nfasta.0.30.cons.summary\nfasta.0.30.cons.names\nfasta.0.30.cons.fasta\nfasta.0.33.cons.summary\nfasta.0.33.cons.names\nfasta.0.33.cons.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_517.dat' fasta.dat && ln -s 'None' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_519.dat' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_518.dat' perotu.otu.dat &&  echo 'consensus.seqs( fasta=fasta.dat ,list=perotu.otu.dat ,count=count.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:14:15.579381", "params": {"cutoff": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\"", "perotu": "{\"use\": \"yes\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 518}]}, \"__current_case__\": 0, \"label\": null}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13712", "id": "89c96313ae93d0a8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_consensus_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "c661245d3c9c7a1b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "c661245d3c9c7a1b", "uuid": "ef8e6508-b2c1-41ba-99a7-48b8f91816aa"}}, "update_time": "2018-02-08T17:14:56.139601", "tool_id": "mothur_cooccurrence", "outputs": {"logfile": {"src": "hda", "id": "691344dc3af3bae5", "uuid": "bf5e2572-adc7-48af-97ba-de7fbc4c5d67"}, "out_summary": {"src": "hda", "id": "9cb939e9f07d29cd", "uuid": "e5d7ca81-706e-4320-8012-af7c59eb71e9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > cooccurrence(shared=otu.dat,metric=cscore,matrixmodel=sim2,iters=1000)\nunique\nInitial c score: 0.505263\n\naverage metric score: 0.49971\nzscore: 0.688308\nstandard deviation: 0.00806771\nnon-parametric p-value: 0.081\n0.01\nInitial c score: 0.505495\n\naverage metric score: 0.499899\nzscore: 0.689761\nstandard deviation: 0.00811162\nnon-parametric p-value: 0.085\n0.02\nInitial c score: 0.505107\n\naverage metric score: 0.499893\nzscore: 0.603707\nstandard deviation: 0.00863748\nnon-parametric p-value: 0.334\n0.03\nInitial c score: 0.505609\n\naverage metric score: 0.500176\nzscore: 0.672499\nstandard deviation: 0.00807817\nnon-parametric p-value: 0.256\n0.04\nInitial c score: 0.506329\n\naverage metric score: 0.500085\nzscore: 0.730838\nstandard deviation: 0.00854372\nnon-parametric p-value: 0.17\n0.05\nInitial c score: 0.507042\n\naverage metric score: 0.499892\nzscore: 0.727804\nstandard deviation: 0.00982421\nnon-parametric p-value: 0.181\n0.06\nInitial c score: 0.508475\n\naverage metric score: 0.499489\nzscore: 0.738319\nstandard deviation: 0.01217\nnon-parametric p-value: 0.097\n0.07\nInitial c score: 0.509091\n\naverage metric score: 0.500385\nzscore: 0.7394\nstandard deviation: 0.0117742\nnon-parametric p-value: 0.106\n0.08\nInitial c score: 0.510638\n\naverage metric score: 0.500255\nzscore: 0.668373\nstandard deviation: 0.0155347\nnon-parametric p-value: 0.241\n0.09\nInitial c score: 0.511111\n\naverage metric score: 0.49986\nzscore: 0.739436\nstandard deviation: 0.0152159\nnon-parametric p-value: 0.117\n0.10\nInitial c score: 0.509756\n\naverage metric score: 0.500649\nzscore: 0.529354\nstandard deviation: 0.0172046\nnon-parametric p-value: 0.488\n0.11\nInitial c score: 0.513514\n\naverage metric score: 0.500045\nzscore: 0.691855\nstandard deviation: 0.0194672\nnon-parametric p-value: 0.262\n0.12\nInitial c score: 0.514286\n\naverage metric score: 0.500101\nzscore: 0.715402\nstandard deviation: 0.0198278\nnon-parametric p-value: 0.262\n0.13\nInitial c score: 0.516129\n\naverage metric score: 0.499629\nzscore: 0.670815\nstandard deviation: 0.024597\nnon-parametric p-value: 0.146\n0.14\nInitial c score: 0.518519\n\naverage metric score: 0.499396\nzscore: 0.660312\nstandard deviation: 0.0289598\nnon-parametric p-value: 0.29\n0.15\nInitial c score: 0.516923\n\naverage metric score: 0.50024\nzscore: 0.594084\nstandard deviation: 0.028082\nnon-parametric p-value: 0.446\n0.16\nInitial c score: 0.513333\n\naverage metric score: 0.499947\nzscore: 0.475889\nstandard deviation: 0.0281298\nnon-parametric p-value: 0.57\n0.17\nInitial c score: 0.513834\n\naverage metric score: 0.500664\nzscore: 0.406264\nstandard deviation: 0.0324173\nnon-parametric p-value: 0.615\n0.18\nInitial c score: 0.514286\n\naverage metric score: 0.499648\nzscore: 0.421505\nstandard deviation: 0.0347281\nnon-parametric p-value: 0.611\n0.19\nInitial c score: 0.51462\n\naverage metric score: 0.499287\nzscore: 0.382877\nstandard deviation: 0.0400476\nnon-parametric p-value: 0.645\n0.20\nInitial c score: 0.514706\n\naverage metric score: 0.501265\nzscore: 0.295044\nstandard deviation: 0.0455565\nnon-parametric p-value: 0.7\n0.21\nInitial c score: 0.525\n\naverage metric score: 0.501542\nzscore: 0.523122\nstandard deviation: 0.0448429\nnon-parametric p-value: 0.55\n0.22\nInitial c score: 0.527473\n\naverage metric score: 0.499813\nzscore: 0.515418\nstandard deviation: 0.0536639\nnon-parametric p-value: 0.582\n0.23\nInitial c score: 0.538462\n\naverage metric score: 0.498821\nzscore: 0.702445\nstandard deviation: 0.0564329\nnon-parametric p-value: 0.425\n0.24\nInitial c score: 0.533333\n\naverage metric score: 0.4974\nzscore: 0.468581\nstandard deviation: 0.0766854\nnon-parametric p-value: 0.65\n0.25\nInitial c score: 0.535714\n\naverage metric score: 0.5005\nzscore: 0.367823\nstandard deviation: 0.095737\nnon-parametric p-value: 0.708\n0.26\nInitial c score: 0.533333\n\naverage metric score: 0.4956\nzscore: 0.288774\nstandard deviation: 0.130667\nnon-parametric p-value: 0.761\n0.27\nInitial c score: 0.533333\n\naverage metric score: 0.4974\nzscore: 0.272986\nstandard deviation: 0.13163\nnon-parametric p-value: 0.776\n0.29\nInitial c score: 0.6\n\naverage metric score: 0.4894\nzscore: 0.65946\nstandard deviation: 0.167713\nnon-parametric p-value: 0.599\n0.32\nInitial c score: 0.5\n\naverage metric score: 0.496\nzscore: 0.0191454\nstandard deviation: 0.208927\nnon-parametric p-value: 0.867\n0.33\nInitial c score: 0.5\n\naverage metric score: 0.499833\nzscore: 0.000833623\nstandard deviation: 0.19993\nnon-parametric p-value: 0.88\n0.36\nInitial c score: 0.666667\n\naverage metric score: 0.503333\nzscore: 0.569652\nstandard deviation: 0.286725\nnon-parametric p-value: 0.755\n0.38\nInitial c score: 1\n\naverage metric score: 0.477\nzscore: 1.04711\nstandard deviation: 0.499471\nnon-parametric p-value: 0.477\n0.41\nInitial c score: 1\n\naverage metric score: 0.52\nzscore: 0.960769\nstandard deviation: 0.4996\nnon-parametric p-value: 0.52\n0.45\nInitial c score: -nan\n\naverage metric score: -nan\nzscore: -nan\nstandard deviation: -nan\nnon-parametric p-value: 0\n0.55\nNot enough OTUs for co-occurrence analysis, skipping\n\nOutput File Names: \notu.cooccurence.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_530.dat' otu.dat &&  echo 'cooccurrence( shared=otu.dat, metric=cscore, matrixmodel=sim2, iters=1000 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:14:52.638168", "params": {"matrixmodel": "\"sim2\"", "iters": "\"1000\"", "metric": "\"cscore\"", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13806", "id": "8b9818d7842d6e75", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cooccurrence.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"metric": "vratio", "otu": {"src": "hda", "id": "f1cb956746b7222f"}, "groups": ["forest", "pasture"], "label": ["0.05", "0.22", "0.41"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "f1cb956746b7222f", "uuid": "2253cdd5-860c-4546-bfcd-80b05a1479c9"}}, "update_time": "2018-02-08T17:15:16.391349", "tool_id": "mothur_cooccurrence", "outputs": {"logfile": {"src": "hda", "id": "9c51eb665ea2103a", "uuid": "12b819be-425e-44e4-91c8-36522b833d89"}, "out_summary": {"src": "hda", "id": "c59b1eb3addb92c6", "uuid": "6650870a-9871-4e0d-aa08-a94a01a4e784"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > cooccurrence(shared=otu.dat,metric=vratio,matrixmodel=sim2,iters=1000,l \rabel=0.05-0.22-0.41,groups=forest-pasture)\n0.05\nInitial c score: 0.0140845\n\naverage metric score: 0.0140845\nzscore: -1\nstandard deviation: 2.98372e-16\nnon-parametric p-value: 1\n0.22\nInitial c score: 0.285714\n\naverage metric score: 0.285714\nzscore: 1\nstandard deviation: 3.27516e-15\nnon-parametric p-value: 1\n0.41\nInitial c score: 0\n\naverage metric score: 0\nzscore: -nan\nstandard deviation: 0\nnon-parametric p-value: 1\n\nOutput File Names: \notu.cooccurence.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_533.dat' otu.dat &&  echo 'cooccurrence( shared=otu.dat, metric=vratio, matrixmodel=sim2, iters=1000 ,label=0.05-0.22-0.41 ,groups=forest-pasture )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:15:13.250684", "params": {"matrixmodel": "\"sim2\"", "iters": "\"1000\"", "metric": "\"vratio\"", "dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.22\", \"0.41\"]", "groups": "[\"forest\", \"pasture\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "13891", "id": "b3dbb33ff37f6ca1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_cooccurrence.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"axes": {"src": "hda", "id": "3511dc9f211ca562"}, "input|source": "shared", "input|otu": {"src": "hda", "id": "b7614d7298eb8371"}}, "job": {"inputs": {"axes": {"src": "hda", "id": "3511dc9f211ca562", "uuid": "ad7e52e8-f6da-42c3-9118-9a115f5f0914"}, "otu": {"src": "hda", "id": "b7614d7298eb8371", "uuid": "b1349374-8445-467e-943b-25973a860ae3"}}, "update_time": "2018-02-08T17:15:37.113599", "tool_id": "mothur_corr_axes", "outputs": {"logfile": {"src": "hda", "id": "c068ba61abe27ec2", "uuid": "51756d9e-0966-4007-b404-9c56634d51fd"}, "corr_axes": {"src": "hda", "id": "751af820aa10c307", "uuid": "923c2fd2-a3bc-40ea-9eb2-abfc3900dc9b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > corr.axes(shared=input.otu.dat,method=pearson,axes=/tmp/saskia/tmpKSDp0 \rp/files/000/dataset_536.dat,numaxes=3)\nYou did not provide a label, I will use the first label in your inputfile.\n\nOutput File Names: \ninput.otu.pearson.corr.axes\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_537.dat' input.otu.dat &&  echo 'corr.axes( shared=input.otu.dat, method=pearson, axes=/tmp/saskia/tmpKSDp0p/files/000/dataset_536.dat, numaxes=3 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:15:33.982854", "params": {"numaxes": "\"3\"", "input": "{\"groups\": null, \"source\": \"shared\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 537}]}, \"__current_case__\": 0, \"label\": null}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"pearson\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14013", "id": "a6edf8654f66f4d6", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_corr_axes.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input|metadata": {"src": "hda", "id": "c2b0116e87929f66"}, "axes": {"src": "hda", "id": "aa43a28a12fcf867"}, "input|source": "metadata"}, "job": {"inputs": {"axes": {"src": "hda", "id": "aa43a28a12fcf867", "uuid": "f4234459-a2f4-4fdb-8fa6-6cbcf5638eb3"}, "metadata": {"src": "hda", "id": "c2b0116e87929f66", "uuid": "2431fcfc-cdbb-4eba-a953-4ee99eaefe3a"}}, "update_time": "2018-02-08T17:15:58.839796", "tool_id": "mothur_corr_axes", "outputs": {"logfile": {"src": "hda", "id": "bb9931d062678360", "uuid": "556cb252-2dda-42fd-9167-6f44e15d12b2"}, "corr_axes": {"src": "hda", "id": "828c366ec88b9842", "uuid": "92def415-ab6a-42f2-935c-c574aad0b57c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > corr.axes(metadata=input.metadata.dat,method=pearson,axes=/tmp/saskia/t \rmpKSDp0p/files/000/dataset_540.dat,numaxes=3)\nYou did not provide a label, I will use the first label in your inputfile.\n\nOutput File Names: \ninput.metadata.pearson.corr.axes\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_541.dat' input.metadata.dat &&  echo 'corr.axes( metadata=input.metadata.dat, method=pearson, axes=/tmp/saskia/tmpKSDp0p/files/000/dataset_540.dat, numaxes=3 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:15:55.632585", "params": {"numaxes": "\"3\"", "input": "{\"source\": \"metadata\", \"__current_case__\": 1, \"metadata\": {\"values\": [{\"src\": \"hda\", \"id\": 541}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"pearson\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14126", "id": "e8a2248405ed0640", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_corr_axes.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input|label": "0.05", "input|source": "shared", "input|groups": ["forest", "pasture"], "axes": {"src": "hda", "id": "76880adb125efe03"}, "input|otu": {"src": "hda", "id": "eafd24481bcc96df"}}, "job": {"inputs": {"axes": {"src": "hda", "id": "76880adb125efe03", "uuid": "49bbc3a7-5968-436f-b8bf-1c7d863a9a9a"}, "otu": {"src": "hda", "id": "eafd24481bcc96df", "uuid": "e53ae831-a4e6-4710-a763-420abb52caf2"}}, "update_time": "2018-02-08T17:16:19.486444", "tool_id": "mothur_corr_axes", "outputs": {"logfile": {"src": "hda", "id": "d36e0ad5b4ecc523", "uuid": "d9f1e3db-30eb-4d51-8fea-d9150db896a8"}, "corr_axes": {"src": "hda", "id": "f71b4098ab6a1836", "uuid": "b0f94268-023d-4674-be3f-a1562438a6fb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > corr.axes(relabund=input.otu.dat,label=0.05,groups=forest-pasture,metho \rd=pearson,axes=/tmp/saskia/tmpKSDp0p/files/000/dataset_544.dat,numaxes=3)\n\nOutput File Names: \ninput.otu.pearson.corr.axes\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_545.dat' input.otu.dat &&  echo 'corr.axes( relabund=input.otu.dat, label=0.05, groups=forest-pasture, method=pearson, axes=/tmp/saskia/tmpKSDp0p/files/000/dataset_544.dat, numaxes=3 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:16:16.360411", "params": {"numaxes": "\"3\"", "input": "{\"groups\": [\"forest\", \"pasture\"], \"source\": \"shared\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 545}]}, \"__current_case__\": 0, \"label\": \"0.05\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"pearson\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14234", "id": "168b8fc92b5c87b9", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_corr_axes.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "2055ef0ee953a321"}}, "job": {"inputs": {"group": {"src": "hda", "id": "2055ef0ee953a321", "uuid": "85f8a4fb-c98f-4e67-959c-8fa7b160350e"}}, "update_time": "2018-02-08T17:16:37.211383", "tool_id": "mothur_count_groups", "outputs": {"logfile": {"src": "hda", "id": "d1010cb72bf991e5", "uuid": "b339060b-210b-4a0e-8ca3-cfaeb05bab93"}, "grp_count": {"src": "hda", "id": "2b91a5aff526e014", "uuid": "330704c8-aa6d-489c-b5e0-4f3a1cd28aa8"}, "summary": {"src": "hda", "id": "39ed0b190e5aa078", "uuid": "be37c436-d733-40aa-9d3b-3ceec97a6a22"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > count.groups(shared=group.dat)\nforest contains 49.\npasture contains 49.\n\nTotal seqs: 98.\n\nOutput File Names: \ngroup.count.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_548.dat' group.dat &&  echo 'count.groups( shared=group.dat )' | sed 's/ //g' | mothur | tee mothur.out.log &&  cat mothur.*.logfile | head -n-7 | sed '1,30d' > '/tmp/saskia/tmpKSDp0p/files/000/dataset_550.dat'", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:16:34.007477", "params": {"groupnames": "{\"source\": \"none\", \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14320", "id": "f28875befd5fbf72", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_count_groups.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"groupnames|groups": ["forest", "pasture"], "group": {"src": "hda", "id": "731d7fc7f6176125"}, "groupnames|source": "groups"}, "job": {"inputs": {"group": {"src": "hda", "id": "731d7fc7f6176125", "uuid": "2fb9ef4d-8299-4dab-abb7-022dac7f5b56"}}, "update_time": "2018-02-08T17:16:49.634091", "tool_id": "mothur_count_groups", "outputs": {"logfile": {"src": "hda", "id": "8710e509865c9aaa", "uuid": "0b718802-5d6d-4b8d-ae15-4b7a7c207bcb"}, "grp_count": {"src": "hda", "id": "64f19a468d4ecfd5", "uuid": "54dfe4be-87cd-4ddd-9a46-7a98f76edb5d"}, "summary": {"src": "hda", "id": "ced3352a0235cd8b", "uuid": "22d85b3f-4e99-41ca-b1b6-525a68e0a595"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > count.groups(shared=group.dat,groups=forest-pasture)\nforest contains 49.\npasture contains 49.\n\nTotal seqs: 98.\n\nOutput File Names: \ngroup.count.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_552.dat' group.dat &&  echo 'count.groups( shared=group.dat ,groups=forest-pasture )' | sed 's/ //g' | mothur | tee mothur.out.log &&  cat mothur.*.logfile | head -n-7 | sed '1,30d' > '/tmp/saskia/tmpKSDp0p/files/000/dataset_554.dat'", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:16:46.402985", "params": {"groupnames": "{\"source\": \"groups\", \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14410", "id": "0805ac7051fb8901", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_count_groups.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"name": {"src": "hda", "id": "2768baa09f52abc1"}}, "job": {"inputs": {"name": {"src": "hda", "id": "2768baa09f52abc1", "uuid": "877d12b1-a9ae-43bd-bd42-826b4b94e910"}}, "update_time": "2018-02-08T17:17:02.896150", "tool_id": "mothur_count_seqs", "outputs": {"logfile": {"src": "hda", "id": "8e15e2c734ba9663", "uuid": "a7bef60f-dcf4-4097-b6cc-dae34ad58be5"}, "seq_count": {"src": "hda", "id": "f4b2790380ce04e0", "uuid": "2c11e730-b181-4268-8b2b-1304ec1671b5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > count.seqs(name=name.dat)\n\nUsing 1 processors.\nIt took 0 secs to create a table for 98 sequences.\n\n\nTotal number of sequences: 98\n\nOutput File Names: \nname.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_556.dat' name.dat &&  echo 'count.seqs( name=name.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:16:59.097828", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "grouping": "{\"use\": \"no\", \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14500", "id": "6b84be122359b58b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_count_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"grouping|group": {"src": "hda", "id": "1e4cd37e942f1647"}, "grouping|use": "yes", "name": {"src": "hda", "id": "2ea80d0e66f18b07"}}, "job": {"inputs": {"group": {"src": "hda", "id": "1e4cd37e942f1647", "uuid": "103a5eb2-d49e-43d3-bac3-ccb2e1a53715"}, "name": {"src": "hda", "id": "2ea80d0e66f18b07", "uuid": "18a1e998-a6c8-4f4f-96dd-24a69a4d7652"}}, "update_time": "2018-02-08T17:17:25.704500", "tool_id": "mothur_count_seqs", "outputs": {"logfile": {"src": "hda", "id": "e57e8f741b8c587a", "uuid": "9bf1e448-c3f1-45f0-9192-20330890bfb6"}, "seq_count": {"src": "hda", "id": "9a68e8442a2ae0ec", "uuid": "efc00a4e-2573-489d-a8dd-58a6193eea62"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > count.seqs(group=grouping.group.dat,name=name.dat)\n\nUsing 1 processors.\nIt took 0 secs to create a table for 98 sequences.\n\n\nTotal number of sequences: 98\n\nOutput File Names: \nname.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_559.dat' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_560.dat' grouping.group.dat &&  echo 'count.seqs( group=grouping.group.dat, name=name.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:17:22.636543", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "grouping": "{\"use\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 560}]}, \"groups\": null, \"__current_case__\": 0}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14615", "id": "eb96e852c39cc9f1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_count_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"grouping|group": {"src": "hda", "id": "ba8874b7e3e0c2f3"}, "grouping|use": "yes", "name": {"src": "hda", "id": "60e341e237cd70c8"}, "grouping|groups": "pasture"}, "job": {"inputs": {"group": {"src": "hda", "id": "ba8874b7e3e0c2f3", "uuid": "536927dc-c192-4c3e-a6eb-a8c2fc4ce4ee"}, "name": {"src": "hda", "id": "60e341e237cd70c8", "uuid": "deb928d4-ad1e-4c1f-8098-30f2aea5b1e5"}}, "update_time": "2018-02-08T17:17:46.294616", "tool_id": "mothur_count_seqs", "outputs": {"logfile": {"src": "hda", "id": "ec153c27faccd8c3", "uuid": "60bf6227-8266-4dff-afe0-b41eddfc98e5"}, "seq_count": {"src": "hda", "id": "7e283a4b4d60f5b4", "uuid": "10feb9e6-0a1b-42a1-a03d-c040f1369ce4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > count.seqs(group=grouping.group.dat,groups=pasture,name=name.dat)\n\nUsing 1 processors.\nIt took 0 secs to create a table for 98 sequences.\n\n\nTotal number of sequences: 98\n\nOutput File Names: \nname.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_563.dat' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_564.dat' grouping.group.dat &&  echo 'count.seqs( group=grouping.group.dat, groups=pasture, name=name.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:17:43.317222", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "grouping": "{\"use\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 564}]}, \"groups\": \"pasture\", \"__current_case__\": 0}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14731", "id": "e63663c4a976dc8c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_count_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"grouping|group": {"src": "hda", "id": "632f677f352f3520"}, "grouping|use": "yes", "name": {"src": "hda", "id": "cdf5fcd4ad6fb5ef"}, "grouping|groups": ["pasture", "forest"]}, "job": {"inputs": {"group": {"src": "hda", "id": "632f677f352f3520", "uuid": "2acbeca9-34f4-4ae5-9bd4-3a8f8d73b8b6"}, "name": {"src": "hda", "id": "cdf5fcd4ad6fb5ef", "uuid": "1883ab42-717c-4697-8567-f10bb2313628"}}, "update_time": "2018-02-08T17:18:06.896417", "tool_id": "mothur_count_seqs", "outputs": {"logfile": {"src": "hda", "id": "723d087f45888e63", "uuid": "30655e8b-a706-46a1-8f4b-907424e4e5a6"}, "seq_count": {"src": "hda", "id": "536b558fd30defca", "uuid": "d6e04181-dee8-45d0-9972-97111e7b319c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > count.seqs(group=grouping.group.dat,groups=pasture-forest,name=name.dat \r)\n\nUsing 1 processors.\nIt took 0 secs to create a table for 98 sequences.\n\n\nTotal number of sequences: 98\n\nOutput File Names: \nname.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_567.dat' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_568.dat' grouping.group.dat &&  echo 'count.seqs( group=grouping.group.dat, groups=pasture-forest, name=name.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:18:03.744174", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "grouping": "{\"use\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 568}]}, \"groups\": [\"pasture\", \"forest\"], \"__current_case__\": 0}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14840", "id": "ea1cd3f6f7bfdbc8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_count_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"nameOrCount": {"src": "hda", "id": "aa616977935bece4"}, "repfasta": {"src": "hda", "id": "b82be0a67dfc3ead"}, "otu": {"src": "hda", "id": "ecbb26f6b49a2189"}, "constaxonomy": {"src": "hda", "id": "c097cce02f6efe06"}, "label": "unique"}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "aa616977935bece4", "uuid": "23d0a8a9-8cd1-4e1f-8066-e4f4c023df8c"}, "repfasta": {"src": "hda", "id": "b82be0a67dfc3ead", "uuid": "0c5fca4c-acb1-4344-91dd-3567a08e7173"}, "otu": {"src": "hda", "id": "ecbb26f6b49a2189", "uuid": "1cc67aa9-8f9f-4d4f-902f-47e2bbafd6a1"}, "constaxonomy": {"src": "hda", "id": "c097cce02f6efe06", "uuid": "44a0f4ed-ce6e-4a99-8c7f-fd15e74d7657"}}, "update_time": "2018-02-08T17:18:33.797429", "tool_id": "mothur_create_database", "outputs": {"logfile": {"src": "hda", "id": "4fcb2862e39bce1b", "uuid": "50452c1e-8865-490b-a150-ca3c4a03c0db"}, "database": {"src": "hda", "id": "0507eab7257c99fb", "uuid": "dd8a2598-7156-4ff5-8dd4-aa02af6af4cb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > create.database(list=otu.dat,repfasta=repfasta.dat,repname=nameOrCount. \rdat,constaxonomy=constaxonomy.dat,label=unique)\n\nOutput File Names: \notu.database\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_571.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_572.dat' repfasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_573.dat' nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_574.dat' constaxonomy.dat && ln -s 'None' group.dat &&  echo 'create.database( list=otu.dat ,repfasta=repfasta.dat ,repname=nameOrCount.dat ,constaxonomy=constaxonomy.dat ,label=unique )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:18:30.660644", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "group": "null", "dbkey": "\"hg17\"", "label": "\"unique\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "14992", "id": "1f643d6293754887", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_create_database.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"nameOrCount": {"src": "hda", "id": "66041b9fc316678f"}, "repfasta": {"src": "hda", "id": "ea961441905a3251"}, "otu": {"src": "hda", "id": "dad37bad3e582a03"}, "constaxonomy": {"src": "hda", "id": "f706247abc458287"}, "label": "unique"}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "66041b9fc316678f", "uuid": "f8944112-9c77-460e-81c2-a543787690b9"}, "repfasta": {"src": "hda", "id": "ea961441905a3251", "uuid": "225fe3e4-bc37-4cb5-95a8-ed3b69f59be8"}, "otu": {"src": "hda", "id": "dad37bad3e582a03", "uuid": "8650be9a-feff-4bdb-8343-002b66ccf18b"}, "constaxonomy": {"src": "hda", "id": "f706247abc458287", "uuid": "063fc1c5-72fa-4744-b007-61c8c5f4ef78"}}, "update_time": "2018-02-08T17:19:01.552810", "tool_id": "mothur_create_database", "outputs": {"logfile": {"src": "hda", "id": "f39983d675d72056", "uuid": "0351c5e2-e001-48a3-a0d4-51c562891382"}, "database": {"src": "hda", "id": "c338e0c0b90362b9", "uuid": "69043eb9-dcfe-4429-8847-34dc04d2e380"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > create.database(list=otu.dat,repfasta=repfasta.dat,count=nameOrCount.da \rt,constaxonomy=constaxonomy.dat,label=unique)\n\nOutput File Names: \notu.database\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_577.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_578.dat' repfasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_579.dat' nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_580.dat' constaxonomy.dat && ln -s 'None' group.dat &&  echo 'create.database( list=otu.dat ,repfasta=repfasta.dat ,count=nameOrCount.dat ,constaxonomy=constaxonomy.dat ,label=unique )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:18:58.396784", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "group": "null", "dbkey": "\"hg17\"", "label": "\"unique\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15165", "id": "73f3912444e9fea9", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_create_database.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "445fd010406004cf"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "445fd010406004cf", "uuid": "350fa411-824d-4347-a194-594deaff7c95"}}, "update_time": "2018-02-08T17:19:19.237084", "tool_id": "mothur_degap_seqs", "outputs": {"logfile": {"src": "hda", "id": "acb17c34a39829bc", "uuid": "e5f43689-a962-449c-984b-3d0bd77b6e20"}, "out_fasta": {"src": "hda", "id": "756973d6ae6b9fe0", "uuid": "0b910abc-af11-48a8-b277-3b80ba2ba8bb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > degap.seqs(fasta=fasta.dat)\n\nUsing 1 processors.\nDegapping sequences from fasta.dat ...\n10\nIt took 0 secs to degap 10 sequences.\n\n\nOutput File Names: \nfasta.ng.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_583.dat' fasta.dat &&  echo 'degap.seqs( fasta=fasta.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:19:16.126712", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15261", "id": "714401c2c9d376cc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_degap_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "e06eaaa480b62987"}, "inputtype|intype": "namesfile", "inputtype|names": {"src": "hda", "id": "bd5643b7bad6c5ee"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "e06eaaa480b62987", "uuid": "dc2e9af9-d7d9-436c-9619-c65fb4a17e58"}, "names": {"src": "hda", "id": "bd5643b7bad6c5ee", "uuid": "f76d6979-2c69-45f4-adb6-e30bd6908377"}}, "update_time": "2018-02-08T17:19:34.833603", "tool_id": "mothur_deunique_seqs", "outputs": {"groups_file": {"src": "hda", "id": "2e05a675c8e4effa", "uuid": "26b8ee44-3d29-4469-b2fd-b87f6522251a"}, "logfile": {"src": "hda", "id": "0326414b4e40019a", "uuid": "d990da53-bd56-4fb2-b0b6-f47de25d7270"}, "out_fasta": {"src": "hda", "id": "533f5f02878a870d", "uuid": "c25ac10e-52b9-49e8-9c10-6cdbe901225b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > deunique.seqs(name=names.dat,fasta=fasta.dat)\n\nOutput File Names: \nfasta.redundant.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_586.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_587.dat' names.dat &&  echo 'deunique.seqs( name=names.dat, fasta=fasta.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:19:31.626015", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "inputtype": "{\"intype\": \"namesfile\", \"names\": {\"values\": [{\"src\": \"hda\", \"id\": 587}]}, \"__current_case__\": 0}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15371", "id": "32b5b014fd8ff7d7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_deunique_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "fea2f59e598c220b"}, "inputtype|intype": "countfile", "inputtype|names": {"src": "hda", "id": "89c39e6bc9d1ed43"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "fea2f59e598c220b", "uuid": "e91472b1-dad8-42dd-94d8-b94dadafed05"}, "names": {"src": "hda", "id": "89c39e6bc9d1ed43", "uuid": "59c434e9-21eb-4c7e-b650-d415e4c681fa"}}, "update_time": "2018-02-08T17:19:55.584258", "tool_id": "mothur_deunique_seqs", "outputs": {"groups_file": {"src": "hda", "id": "78187af971523bc5", "uuid": "a69e189f-7e4c-4720-bb47-ca41b7bcb0fc"}, "logfile": {"src": "hda", "id": "808438a09599e30a", "uuid": "172c6010-537e-44eb-a61d-c7d8ead283ea"}, "out_fasta": {"src": "hda", "id": "5f0fd33b40be7b90", "uuid": "29cc005e-a38f-4461-9f5a-7f6fec1ff42d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > deunique.seqs(count=names.dat,fasta=fasta.dat)\n\nOutput File Names: \nfasta.redundant.fasta\nnames.redundant.groups\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_591.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_592.dat' names.dat &&  echo 'deunique.seqs( count=names.dat, fasta=fasta.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:19:52.400579", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "inputtype": "{\"intype\": \"countfile\", \"names\": {\"values\": [{\"src\": \"hda\", \"id\": 592}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15487", "id": "b722e15494aaed88", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_deunique_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "0fd8e817110724fa"}, "inputtype|intype": "countfile", "inputtype|names": {"src": "hda", "id": "8cf2c4d96fac8f30"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "0fd8e817110724fa", "uuid": "0ab27f57-35d3-414a-b873-a2a3638f8dc3"}, "names": {"src": "hda", "id": "8cf2c4d96fac8f30", "uuid": "2d94fcfa-9ec9-49e5-b797-a27b3680b1f3"}}, "update_time": "2018-02-08T17:20:21.581063", "tool_id": "mothur_deunique_seqs", "outputs": {"groups_file": {"src": "hda", "id": "26a7a34cb9e5bfcc", "uuid": "6ff5666d-cc51-457d-9faa-68081fcbbf0a"}, "logfile": {"src": "hda", "id": "d0739bd14cbff0fb", "uuid": "15127adf-a761-4cd5-b404-0dd5aefac5fa"}, "out_fasta": {"src": "hda", "id": "aaec100bcea4a774", "uuid": "6b20f501-a458-4912-84a8-f1f5db2ee785"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > deunique.seqs(count=names.dat,fasta=fasta.dat)\n\nOutput File Names: \nfasta.redundant.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_596.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_597.dat' names.dat &&  echo 'deunique.seqs( count=names.dat, fasta=fasta.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:20:18.330376", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "inputtype": "{\"intype\": \"countfile\", \"names\": {\"values\": [{\"src\": \"hda\", \"id\": 597}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15598", "id": "3837873dd5f5f1f7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_deunique_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"tree": {"src": "hda", "id": "ed97b3e2ab207f95"}, "names": {"src": "hda", "id": "3e9d65cd9bd3cb5b"}}, "job": {"inputs": {"tree": {"src": "hda", "id": "ed97b3e2ab207f95", "uuid": "8171afc5-b70b-43d9-8cb2-54983b923226"}, "names": {"src": "hda", "id": "3e9d65cd9bd3cb5b", "uuid": "afc58f8a-27fd-448f-b908-bd15cad5024d"}}, "update_time": "2018-02-08T17:20:47.056523", "tool_id": "mothur_deunique_tree", "outputs": {"logfile": {"src": "hda", "id": "8733d0796a352268", "uuid": "49007554-1f8e-40d2-b876-b55356ff1837"}, "out_tree": {"src": "hda", "id": "9fbd2c401152ab55", "uuid": "440ed4e6-2f7e-4907-b481-13820836e2ad"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > deunique.tree(tree=tree.dat,name=names.dat)\n\nOutput File Names: \ntree.deunique.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_601.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_602.dat' names.dat &&  echo 'deunique.tree( tree=tree.dat, name=names.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:20:43.954435", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15720", "id": "12eb47432b3fa224", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_deunique_tree.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "4611eaf69222f4fc"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "4611eaf69222f4fc", "uuid": "e855b896-9810-401a-b333-c4e23384496d"}}, "update_time": "2018-02-08T17:20:59.418904", "tool_id": "mothur_dist_seqs", "outputs": {"logfile": {"src": "hda", "id": "11f90d7d2e7018d3", "uuid": "92e6a2d8-dc1e-4fae-bd9b-fc4cd45473ac"}, "out_dist": {"src": "hda", "id": "e310ea5c66f14aec", "uuid": "dd2805ef-d7e6-4ea6-8c2e-75f8d788f8f9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > dist.seqs(fasta=fasta.dat,countends=true,processors=1)\n\nUsing 1 processors.\n0\t0\n31\t0\n\nOutput File Names: \nfasta.dist\n\nIt took 0 seconds to calculate the distances for 32 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_605.dat' fasta.dat &&  echo 'dist.seqs( fasta=fasta.dat, countends=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:20:56.286624", "params": {"cutoff": "\"\"", "countends": "\"true\"", "dbkey": "\"hg17\"", "output": "\"\"", "calc": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15806", "id": "6194a3cf14a0177a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_dist_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"cutoff": "0.3", "fasta": {"src": "hda", "id": "3d3fb87387ce837c"}, "calc": "nogaps", "countends": false, "output": "lt"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "3d3fb87387ce837c", "uuid": "e197838d-144e-44fb-bac1-ca8ec8e3b339"}}, "update_time": "2018-02-08T17:21:16.984539", "tool_id": "mothur_dist_seqs", "outputs": {"logfile": {"src": "hda", "id": "619ac1d452a0c845", "uuid": "083fae16-a130-4737-91eb-0fef578c6f86"}, "out_dist": {"src": "hda", "id": "e150414f34961064", "uuid": "dc360c82-95d6-45f2-9ba7-591e518829a7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > dist.seqs(fasta=fasta.dat,calc=nogaps,countends=false,cutoff=0.3,output \r=lt,processors=1)\n\nUsing 1 processors.\n0\t0\n31\t0\n\nOutput File Names: \nfasta.phylip.dist\n\nIt took 0 seconds to calculate the distances for 32 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_608.dat' fasta.dat &&  echo 'dist.seqs( fasta=fasta.dat, calc=nogaps, countends=false, cutoff=0.3, output=lt, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:21:13.826483", "params": {"cutoff": "\"0.3\"", "countends": "\"false\"", "dbkey": "\"hg17\"", "output": "\"lt\"", "calc": "\"nogaps\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "15891", "id": "ce239e512e8f2197", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_dist_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "24493ccad6413f6e"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "24493ccad6413f6e", "uuid": "11f606c6-1b88-4fbc-a277-1b2d16fc55a2"}}, "update_time": "2018-02-08T17:21:38.102240", "tool_id": "mothur_dist_shared", "outputs": {"__new_primary_file_thetayc.unique.lt|jclass.0.18.lt__": {"src": "hda", "id": "0a063fcbe434cf24", "uuid": "6fd33918-5c64-4b5f-b40b-bce477f11d44"}, "__new_primary_file_thetayc.unique.lt|jclass.0.32.lt__": {"src": "hda", "id": "c7f95f7f9cd38954", "uuid": "63ade87b-4250-48bc-a55e-3a01cec0669b"}, "__new_primary_file_thetayc.unique.lt|jclass.0.24.lt__": {"src": "hda", "id": "0ab5259e4af4b72d", "uuid": "3a5a830b-ff9f-4f6f-8a24-4211042cfd6e"}, "__new_primary_file_thetayc.unique.lt|jclass.0.36.lt__": {"src": "hda", "id": "38956bd0aa358c3f", "uuid": "61d147dc-9a9c-474a-b48d-e1ad6330fcb7"}, "__new_primary_file_thetayc.unique.lt|jclass.0.38.lt__": {"src": "hda", "id": "4ece32d755307fe6", "uuid": "a0d2a58a-39b1-4a2f-a7d8-38679890e1e2"}, "__new_primary_file_thetayc.unique.lt|thetayc.0.02.lt__": {"src": "hda", "id": "f85272b32a0e3096", "uuid": "9ac744ce-34a1-495f-9637-c9b08543095e"}, "__new_primary_file_thetayc.unique.lt|thetayc.0.14.lt__": {"src": "hda", "id": "311536be0a100aff", "uuid": 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"__new_primary_file_thetayc.unique.lt|thetayc.0.21.lt__": {"src": "hda", "id": "b55d88427b65723f", "uuid": "8eff059b-de68-4d40-acd1-210d558a3b81"}, "__new_primary_file_thetayc.unique.lt|thetayc.unique.lt__": {"src": "hda", "id": "d19d4ec68e7448b5", "uuid": "7f768e59-7cb6-4a7d-bc9e-1227f3a56372"}, "__new_primary_file_thetayc.unique.lt|thetayc.0.19.lt__": {"src": "hda", "id": "d1af14f4da906d66", "uuid": "be3446ce-69c6-49b1-9c97-667f153ac558"}, "__new_primary_file_thetayc.unique.lt|jclass.0.15.lt__": {"src": "hda", "id": "825dec33847777b5", "uuid": "adb13a7f-e79e-4b3f-9f42-47430d91174d"}, "__new_primary_file_thetayc.unique.lt|jclass.0.16.lt__": {"src": "hda", "id": "ee234bf95ca1c311", "uuid": "55f3b565-c35a-446f-acda-1a80a908b9e7"}, "__new_primary_file_thetayc.unique.lt|jclass.0.20.lt__": {"src": "hda", "id": "53dfc6f5f1ee9e8c", "uuid": "fcec0cce-78e6-4410-a5b4-60ea38791156"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > dist.shared(shared=otu.dat,calc=jclass-thetayc,output=lt,processors=1)\n\nUsing 1 processors.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: 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> quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_611.dat' otu.dat &&  echo 'dist.shared( shared=otu.dat, calc=jclass-thetayc, output=lt, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:21:31.443852", "params": {"dbkey": "\"hg17\"", "label": "null", "groups": "null", "output": "\"lt\"", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "calc": "[\"jclass\", \"thetayc\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": 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{"src": "hda", "id": "a4a6e47454aeba8e", "uuid": "35129200-5454-46ab-9498-584451cb60fd"}, "__new_primary_file_whittaker.0.22.lt|structpearson.0.22.lt__": {"src": "hda", "id": "45a4f11c8f7e7223", "uuid": "2bdde3cd-797c-40d3-bd31-70325d55d785"}, "__new_primary_file_whittaker.0.22.lt|sharednseqs.0.22.lt__": {"src": "hda", "id": "b726424360e35364", "uuid": "1d58ebaa-35df-4000-8fb3-966eb5384dc0"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > dist.shared(shared=otu.dat,label=0.05-0.22,groups=forest-pasture,calc=s \rharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-k \rstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-memeuclid \rean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-canberra-g \rower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-structchi2-structe \ruclidean-structpearson-sharednseqs-sharedobserved,output=lt,processors=1)\n\nUsing 1 processors.\nsharedobserved is not a valid estimator for the matrix.output command and will be disregarded. Valid estimators are anderberg, braycurtis, canberra, gower, hamming, hellinger, jabund, jclass, jest, jsd, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, rjsd, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker, \n0.05\n0.22\n\nOutput File Names: \notu.sharedsobs.0.05.lt.dist\notu.sharedchao.0.05.lt.dist\notu.sharedace.0.05.lt.dist\notu.anderberg.0.05.lt.dist\notu.jclass.0.05.lt.dist\notu.jest.0.05.lt.dist\notu.kulczynski.0.05.lt.dist\notu.kulczynskicody.0.05.lt.dist\notu.kstest.0.05.lt.dist\notu.lennon.0.05.lt.dist\notu.ochiai.0.05.lt.dist\notu.sorclass.0.05.lt.dist\notu.sorest.0.05.lt.dist\notu.whittaker.0.05.lt.dist\notu.hamming.0.05.lt.dist\notu.memchi2.0.05.lt.dist\notu.memchord.0.05.lt.dist\notu.memeuclidean.0.05.lt.dist\notu.mempearson.0.05.lt.dist\notu.braycurtis.0.05.lt.dist\notu.jabund.0.05.lt.dist\notu.morisitahorn.0.05.lt.dist\notu.sorabund.0.05.lt.dist\notu.thetan.0.05.lt.dist\notu.thetayc.0.05.lt.dist\notu.canberra.0.05.lt.dist\notu.gower.0.05.lt.dist\notu.hellinger.0.05.lt.dist\notu.manhattan.0.05.lt.dist\notu.odum.0.05.lt.dist\notu.soergel.0.05.lt.dist\notu.spearman.0.05.lt.dist\notu.speciesprofile.0.05.lt.dist\notu.structchi2.0.05.lt.dist\notu.structeuclidean.0.05.lt.dist\notu.structpearson.0.05.lt.dist\notu.sharednseqs.0.05.lt.dist\notu.sharedsobs.0.22.lt.dist\notu.sharedchao.0.22.lt.dist\notu.sharedace.0.22.lt.dist\notu.anderberg.0.22.lt.dist\notu.jclass.0.22.lt.dist\notu.jest.0.22.lt.dist\notu.kulczynski.0.22.lt.dist\notu.kulczynskicody.0.22.lt.dist\notu.kstest.0.22.lt.dist\notu.lennon.0.22.lt.dist\notu.ochiai.0.22.lt.dist\notu.sorclass.0.22.lt.dist\notu.sorest.0.22.lt.dist\notu.whittaker.0.22.lt.dist\notu.hamming.0.22.lt.dist\notu.memchi2.0.22.lt.dist\notu.memchord.0.22.lt.dist\notu.memeuclidean.0.22.lt.dist\notu.mempearson.0.22.lt.dist\notu.braycurtis.0.22.lt.dist\notu.jabund.0.22.lt.dist\notu.morisitahorn.0.22.lt.dist\notu.sorabund.0.22.lt.dist\notu.thetan.0.22.lt.dist\notu.thetayc.0.22.lt.dist\notu.canberra.0.22.lt.dist\notu.gower.0.22.lt.dist\notu.hellinger.0.22.lt.dist\notu.manhattan.0.22.lt.dist\notu.odum.0.22.lt.dist\notu.soergel.0.22.lt.dist\notu.spearman.0.22.lt.dist\notu.speciesprofile.0.22.lt.dist\notu.structchi2.0.22.lt.dist\notu.structeuclidean.0.22.lt.dist\notu.structpearson.0.22.lt.dist\notu.sharednseqs.0.22.lt.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_685.dat' otu.dat &&  echo 'dist.shared( shared=otu.dat, label=0.05-0.22, groups=forest-pasture, calc=sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-kstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-memeuclidean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-canberra-gower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-structchi2-structeuclidean-structpearson-sharednseqs-sharedobserved, output=lt, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:21:58.880697", "params": {"dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.22\"]", "groups": "[\"forest\", \"pasture\"]", "output": "\"lt\"", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"anderberg\", \"jclass\", \"jest\", \"kulczynski\", \"kulczynskicody\", \"kstest\", \"lennon\", \"ochiai\", \"sorclass\", \"sorest\", \"whittaker\", \"hamming\", \"memchi2\", \"memchord\", \"memeuclidean\", \"mempearson\", \"braycurtis\", \"jabund\", \"morisitahorn\", \"sorabund\", \"thetan\", \"thetayc\", \"canberra\", \"gower\", \"hellinger\", \"manhattan\", \"odum\", \"soergel\", \"spearman\", \"speciesprofile\", \"structchi2\", \"structeuclidean\", \"structpearson\", \"sharednseqs\", \"sharedobserved\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16068", "id": "90653ba0c3bbef25", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_dist_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"output": "square", "calc": "canberra", "otu": {"src": "hda", "id": "baf2364ee29b3107"}, "subsampling|use": "yes", "label": ["0.03", "0.33"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "baf2364ee29b3107", "uuid": "d4951c32-9e65-48e0-a3e6-c87cd597d149"}}, "update_time": "2018-02-08T17:22:29.803485", "tool_id": "mothur_dist_shared", "outputs": {"__new_primary_file_canberra.0.33.square.std|canberra.0.03.square.ave__": {"src": "hda", "id": "0cc52239f966e8d8", "uuid": "1e0e7251-b715-4310-9902-f07e202040a9"}, "__new_primary_file_canberra.0.33.square.std|canberra.0.33.square__": {"src": "hda", "id": "26abeaa977847256", "uuid": "24dd2c79-5195-41b7-a6db-cb56d8fe607f"}, "__new_primary_file_canberra.0.33.square.std|canberra.0.33.square.ave__": {"src": "hda", "id": "20daa85480c5e233", "uuid": "c644c065-62d7-4f8c-b217-9b8a45e0d06c"}, "__new_primary_file_canberra.0.33.square.std|canberra.0.33.square.std__": {"src": "hda", "id": "68b1b014e79dbbac", "uuid": "0bee9b58-e601-4cdc-9005-442df905d104"}, "__new_primary_file_canberra.0.33.square.std|canberra.0.03.square__": {"src": "hda", "id": "9aa847d0f9b17c8b", "uuid": "7fc00040-a3e2-44b2-814f-12d3f0f9c5e7"}, "logfile": {"src": "hda", "id": "b46b161a6298a88e", "uuid": "00339ae5-b634-4c23-8bd4-3ba23fb04806"}, "__new_primary_file_canberra.0.33.square.std|canberra.0.03.square.std__": {"src": "hda", "id": "4a18607ffedf0072", "uuid": "799afe6d-3a56-4571-a4a0-ebcb0ad5a168"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > dist.shared(shared=otu.dat,label=0.03-0.33,calc=canberra,subsample=T,it \rers=1000,output=square,processors=1)\n\nUsing 1 processors.\n0.03\n100\n200\n300\n400\n500\n600\n700\n800\n900\n1000\n0.33\n100\n200\n300\n400\n500\n600\n700\n800\n900\n1000\n\nOutput File Names: \notu.canberra.0.03.square.dist\notu.canberra.0.03.square.ave.dist\notu.canberra.0.03.square.std.dist\notu.canberra.0.33.square.dist\notu.canberra.0.33.square.ave.dist\notu.canberra.0.33.square.std.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_761.dat' otu.dat &&  echo 'dist.shared( shared=otu.dat, label=0.03-0.33, calc=canberra, subsample=T, iters=1000, output=square, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:22:26.360733", "params": {"dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.33\"]", "groups": "null", "output": "\"square\"", "subsampling": "{\"iters\": \"1000\", \"subsample\": \"\", \"use\": \"yes\", \"__current_case__\": 0}", "calc": "\"canberra\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16161", "id": "06bb318fcaf8f1eb", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_dist_shared.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"subsampling|use": "yes", "label": "0.10", "otu": {"src": "hda", "id": "cfc54229b67d91e3"}, "subsampling|subsample": "2", "output": "square", "calc": "canberra", "subsampling|iters": "42"}, "job": {"inputs": {"otu": {"src": "hda", "id": "cfc54229b67d91e3", "uuid": "20daefca-def5-4876-946d-4cf232dfb9b0"}}, "update_time": "2018-02-08T17:22:47.020234", "tool_id": "mothur_dist_shared", "outputs": {"__new_primary_file_canberra.0.10.square.std|canberra.0.10.square.ave__": {"src": "hda", "id": "e6723b9768a74d82", "uuid": "79dcde89-0d4b-440f-ad9b-335794b42c15"}, "logfile": {"src": "hda", "id": "71eba17e79d46ea5", "uuid": "bcc4be41-17fa-4a06-b847-718aa331d440"}, "__new_primary_file_canberra.0.10.square.std|canberra.0.10.square__": {"src": "hda", "id": "617cf9f340bd6e86", "uuid": "2ce97851-6f4d-4494-9ef3-797b888ad973"}, "__new_primary_file_canberra.0.10.square.std|canberra.0.10.square.std__": {"src": "hda", "id": "ed1b8cbf308ff665", "uuid": "d49683ab-1105-4341-983b-1203f49ab877"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > dist.shared(shared=otu.dat,label=0.10,calc=canberra,subsample=2,iters=4 \r2,output=square,processors=1)\n\nUsing 1 processors.\n0.10\n\nOutput File Names: \notu.canberra.0.10.square.dist\notu.canberra.0.10.square.ave.dist\notu.canberra.0.10.square.std.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_769.dat' otu.dat &&  echo 'dist.shared( shared=otu.dat, label=0.10, calc=canberra, subsample=2, iters=42, output=square, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:22:43.797807", "params": {"dbkey": "\"hg17\"", "label": "\"0.10\"", "groups": "null", "output": "\"square\"", "subsampling": "{\"iters\": \"42\", \"subsample\": \"2\", \"use\": \"yes\", \"__current_case__\": 0}", "calc": "\"canberra\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16253", "id": "dec5e0baf08c9f80", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_dist_shared.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"oligo|add": "no", "fastq": {"src": "hda", "id": "e033f1f6a16a5fdb"}, "pacbio": false, "format": "sanger"}, "job": {"inputs": {"fastq": {"src": "hda", "id": "e033f1f6a16a5fdb", "uuid": "77438fba-535e-4216-8327-0e768915addb"}}, "update_time": "2018-02-08T17:23:04.684646", "tool_id": "mothur_fastq_info", "outputs": {"qfile_out": {"src": "hda", "id": "6c35ab7e615cea5a", "uuid": "dcefa944-94d0-4b60-97bd-2c4dc8eaecd0"}, "qfile_scrap_out": {"src": "hda", "id": "030656b247de0efe", "uuid": "9b1c11b7-5927-4d58-8b93-e90c055527c0"}, "fasta_scrap_out": {"src": "hda", "id": "a32e6dbc1964b80f", "uuid": "10697ffc-6f5b-49e7-9485-bdcba92bedeb"}, "fasta_out": {"src": "hda", "id": "f691a5951523571b", "uuid": "ed80280c-a610-4d2a-8521-7b0cde8c8754"}, "logfile": {"src": "hda", "id": "aa4dc5fa9f74231b", "uuid": "22ec9601-e7f9-40ca-b8d9-171c3ecbc0bd"}, "fastq_scrap_out": {"src": "hda", "id": "824db84bb730ff40", "uuid": "267a7c53-6bc5-4dde-850b-682f61bf72f7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > fastq.info(fastq=fastq.dat,pacbio=false,format=sanger)\n25\n\nOutput File Names: \nfastq.fasta\nfastq.qual\n\n[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_774.dat' fastq.dat &&  echo 'fastq.info( fastq=fastq.dat, pacbio=false, format=sanger )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:23:01.321492", "params": {"oligo": "{\"add\": \"no\", \"__current_case__\": 1}", "format": "\"sanger\"", "pacbio": "\"false\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16337", "id": "01949e60fe484dc7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_fastq_info.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"oligo|tdiffs": "3", "oligo|oligos": {"src": "hda", "id": "35610b944eae1662"}, "format": "sanger", "oligo|add": "yes", "fastq": {"src": "hda", "id": "bf2647e7c02a9611"}, "oligo|pdiffs": "3", "pacbio": false, "oligo|sdiffs": "7", "oligo|bdiffs": "1", "oligo|ldiffs": "3"}, "job": {"inputs": {"oligos": {"src": "hda", "id": "35610b944eae1662", "uuid": "81848543-318d-40ec-9f24-7e56a060ab4d"}, "fastq": {"src": "hda", "id": "bf2647e7c02a9611", "uuid": "7809aabd-ef88-4cbe-9bed-d0d4bde19717"}}, "update_time": "2018-02-08T17:23:25.374084", "tool_id": "mothur_fastq_info", "outputs": {"qfile_out": {"src": "hda", "id": "fdd788dd2ce60116", "uuid": "0d1ddeba-9f32-4378-9f89-54550cfe540f"}, "qfile_scrap_out": {"src": "hda", "id": "d1ff5636c3d156c1", "uuid": "ecc11736-d5b3-433a-99a7-5bfe26291fd9"}, "fasta_scrap_out": {"src": "hda", "id": "0a9daec53650332d", "uuid": "3ced0477-7b8f-4826-9fa3-dc8c00c7c3a9"}, "fasta_out": {"src": "hda", "id": "0f7bfbeda1808692", "uuid": "439b73c1-c987-439f-b470-01fca30b9187"}, "logfile": {"src": "hda", "id": "8e338a85ec192878", "uuid": "39bb7c9b-3632-4e54-a7af-06f6f0ced455"}, "fastq_scrap_out": {"src": "hda", "id": "32e4cd7ce068c585", "uuid": "4265a7df-7cb5-49ab-9add-e74293195c8a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > fastq.info(fastq=fastq.dat,pacbio=false,format=sanger,oligos=oligo.olig \ros.dat,bdiffs=1,pdiffs=3,tdiffs=3,ldiffs=3,sdiffs=7)\n25\n\nOutput File Names: \nfastq.fasta\nfastq.qual\nfastq.scrap.fastq\nfastq.scrap.fasta\nfastq.scrap.qual\n\n[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_781.dat' fastq.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_782.dat' oligo.oligos.dat &&  echo 'fastq.info( fastq=fastq.dat, pacbio=false, format=sanger ,oligos=oligo.oligos.dat ,bdiffs=1 ,pdiffs=3 ,tdiffs=3 ,ldiffs=3 ,sdiffs=7 )' | sed 's/ //g' | mothur | tee mothur.out.log && mv fastq.scrap.fasta scrap.fasta && mv fastq.scrap.qual scrap.qual", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:23:21.806144", "params": {"oligo": "{\"bdiffs\": \"1\", \"sdiffs\": \"7\", \"ldiffs\": \"3\", \"pdiffs\": \"3\", \"tdiffs\": \"3\", \"add\": \"yes\", \"__current_case__\": 0, \"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 782}]}}", "format": "\"sanger\"", "pacbio": "\"false\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16448", "id": "10a6a0683c3e243b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_fastq_info.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"oligo|tdiffs": "3", "oligo|oligos": {"src": "hda", "id": "1380d0b9d445228e"}, "format": "sanger", "oligo|add": "yes", "fastq": {"src": "hda", "id": "9926857060044181"}, "oligo|pdiffs": "3", "pacbio": false, "oligo|sdiffs": "7", "oligo|bdiffs": "1", "oligo|ldiffs": "3"}, "job": {"inputs": {"oligos": {"src": "hda", "id": "1380d0b9d445228e", "uuid": "8c307d4a-4b92-49ff-a385-b7e66a389056"}, "fastq": {"src": "hda", "id": "9926857060044181", "uuid": "eaf7180b-c799-4fd3-b0c0-e3813deaac9d"}}, "update_time": "2018-02-08T17:24:09.682399", "tool_id": "mothur_fastq_info", "outputs": {"qfile_out": {"src": "hda", "id": "1c98d06fd14cd58f", "uuid": "890802e0-d230-4124-8616-65dc4330f583"}, "qfile_scrap_out": {"src": "hda", "id": "743a8d5f0b93543f", "uuid": "8fd611e9-658c-4b48-b9c7-2bc7030b1ffa"}, "fasta_scrap_out": {"src": "hda", "id": "d2877f6f2610c2e2", "uuid": "8b46de15-d1f8-476f-b274-7dae66d698af"}, "fasta_out": {"src": "hda", "id": "0127e3e8a6471eea", "uuid": "c62929d1-5324-4bd1-b277-4e260a3f43d1"}, "logfile": {"src": "hda", "id": "36389a8523644138", "uuid": "edadd9bc-8711-4aa2-b098-b0871e3c3982"}, "fastq_scrap_out": {"src": "hda", "id": "da235095819aad8a", "uuid": "4ac12252-aa96-4911-90a0-c582f5cadc8c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > fastq.info(fastq=fastq.dat,pacbio=false,format=sanger,oligos=oligo.olig \ros.dat,bdiffs=1,pdiffs=3,tdiffs=3,ldiffs=3,sdiffs=7)\n[WARNING]: your oligos file does not contain any group names.  mothur will not create a groupfile.\n25\n\nOutput File Names: \nfastq.fasta\nfastq.qual\nfastq.scrap.fastq\nfastq.scrap.fasta\nfastq.scrap.qual\n\n[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 2 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_789.dat' fastq.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_790.dat' oligo.oligos.dat &&  echo 'fastq.info( fastq=fastq.dat, pacbio=false, format=sanger ,oligos=oligo.oligos.dat ,bdiffs=1 ,pdiffs=3 ,tdiffs=3 ,ldiffs=3 ,sdiffs=7 )' | sed 's/ //g' | mothur | tee mothur.out.log && mv fastq.scrap.fasta scrap.fasta && mv fastq.scrap.qual scrap.qual", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:24:05.898702", "params": {"oligo": "{\"bdiffs\": \"1\", \"sdiffs\": \"7\", \"ldiffs\": \"3\", \"pdiffs\": \"3\", \"tdiffs\": \"3\", \"add\": \"yes\", \"__current_case__\": 0, \"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 790}]}}", "format": "\"sanger\"", "pacbio": "\"false\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16578", "id": "e4a1e6f57e384175", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_fastq_info.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "8cd4beb5cf8a2f93"}, "inputs_0|fasta": {"src": "hda", "id": "c6b012dc2ec4a20b"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "8cd4beb5cf8a2f93", "uuid": "c9633e87-92ec-41e8-8681-cd3853616f18"}, "inputs_0|fasta": {"src": "hda", "id": "c6b012dc2ec4a20b", "uuid": "f202689a-78a7-4f16-a06c-193c6b7cadb5"}}, "update_time": "2018-02-08T17:24:28.595502", "tool_id": "mothur_filter_seqs", "outputs": {"__new_primary_file_Mock_S280_L001_R1_001_small.trim.contigs.good.align_head|HMP_MOCK.v35.align__": {"src": "hda", "id": "d12daff1a3ddfe3f", "uuid": "59b94fbc-28e9-478b-a3be-6f31b037432e"}, "__new_primary_file_Mock_S280_L001_R1_001_small.trim.contigs.good.align_head|Mock_S280_L001_R1_001_small.trim.contigs.good.align_head__": {"src": "hda", "id": "c9ec74100d9952dd", "uuid": "efb1b48b-884a-432c-b896-0f79354137c3"}, "logfile": {"src": "hda", "id": "e81ccf1738866a34", "uuid": "5253fc43-d4ff-48b4-b4bb-318955c58886"}, "out_filter": {"src": "hda", "id": "e400af07ae3fa77f", "uuid": "3d6ac024-1b0e-47fc-bcfc-4e19cf5b1c57"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > filter.seqs(fasta=fasta.dat-fasta0.dat,vertical=true,soft=0,processors= \r1)\n\nUsing 1 processors.\nCreating Filter... \n32\n10\n\n\nRunning Filter... \n32\n10\n\n\n\nLength of filtered alignment: 553\nNumber of columns removed: 49447\nLength of the original alignment: 50000\nNumber of sequences used to construct filter: 42\n\nOutput File Names: \nfastafasta0.filter\nfasta.filter.fasta\nfasta0.filter.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_797.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_798.dat' fasta0.dat && ln -s 'None' hard.dat &&  echo 'filter.seqs( fasta=fasta.dat-fasta0.dat, vertical=true, soft=0, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log &&  mv fasta.filter.fasta \"HMP_MOCK.v35.align\".filter.fasta && mv fasta0.filter.fasta \"Mock_S280_L001_R1_001_small.trim.contigs.good.align_head\".filter.fasta", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:24:25.233007", "params": {"inputs": "[{\"__index__\": 0, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 798}]}}]", "trump": "\"\"", "vertical": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "hard": "null", "dbkey": "\"hg17\"", "soft": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16693", "id": "3318d523831bcec2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_filter_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "d9eeaf6b2b0ea17f"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "d9eeaf6b2b0ea17f", "uuid": "d7d2e1f4-b3aa-4e9a-8a9b-cbffc910044f"}}, "update_time": "2018-02-08T17:24:49.016571", "tool_id": "mothur_filter_seqs", "outputs": {"filteredfasta": {"src": "hda", "id": "92afd254baae3cac", "uuid": "be76b447-ba3b-42ca-b0ea-02f97b7c93a5"}, "logfile": {"src": "hda", "id": "dc72314d29258a13", "uuid": "d09ac3a3-1577-4b8a-a837-2c45eb5a49f5"}, "out_filter": {"src": "hda", "id": "766e222ad152fb61", "uuid": "c46e69b4-a17e-43f6-a069-7b1a71eee36c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > filter.seqs(fasta=fasta.dat,vertical=true,soft=0,processors=1)\n\nUsing 1 processors.\nCreating Filter... \n32\n\n\nRunning Filter... \n32\n\n\n\nLength of filtered alignment: 553\nNumber of columns removed: 49447\nLength of the original alignment: 50000\nNumber of sequences used to construct filter: 32\n\nOutput File Names: \nfasta.filter\nfasta.filter.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_803.dat' fasta.dat && ln -s 'None' hard.dat &&  echo 'filter.seqs( fasta=fasta.dat, vertical=true, soft=0, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log &&  mv fasta.filter.fasta \"HMP_MOCK.v35.align\".filter.fasta", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:24:45.943706", "params": {"inputs": "[]", "trump": "\"\"", "vertical": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "hard": "null", "dbkey": "\"hg17\"", "soft": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16789", "id": "2c6815fe89528bcf", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_filter_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "4a879c43cb8448df"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "4a879c43cb8448df", "uuid": "82a3f9b7-2c8c-4581-99a3-28ee8ab509cf"}}, "update_time": "2018-02-08T17:25:01.250499", "tool_id": "mothur_filter_shared", "outputs": {"__new_primary_file_unique|unique__": {"src": "hda", "id": "093ebc9d412c603b", "uuid": "768abf77-cedd-4a5a-bddc-0b554cdf7081"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "b20d09ab9f40b4f6", "uuid": "2871a8d8-7e54-446f-b6b7-903707315190"}, "logfile": {"src": "hda", "id": "e39481c9f084a332", "uuid": "457b2a64-4e88-40ac-8c94-eb99e65a950c"}, "__new_primary_file_unique|0.10__": {"src": "hda", "id": "aab4584d69f5e8dc", "uuid": "3e67925b-3f5d-433f-9a0c-95ba91b13bab"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "ab005d4cdb71cef2", "uuid": "0a08a2d9-2415-4eb2-a834-bb5367999485"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > filter.shared(shared=otu.dat,minabund=0,minpercent=0,rarepercent=0,keep \rties=true,minnumsamples=0,minpercentsamples=0,mintotal=0,makerare=true)\nunique\n\nRemoved 0 OTUs.\n0.03\n\nRemoved 0 OTUs.\n0.05\n\nRemoved 0 OTUs.\n0.10\n\nRemoved 0 OTUs.\n\nOutput File Names: \notu.unique.filter.dat\notu.0.03.filter.dat\notu.0.05.filter.dat\notu.0.10.filter.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_807.dat' otu.dat &&  echo 'filter.shared( shared=otu.dat, minabund=0, minpercent=0, rarepercent=0, keepties=true, minnumsamples=0, minpercentsamples=0, mintotal=0, makerare=true )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:24:58.042706", "params": {"rarepercent": "\"0\"", "mintotal": "\"0\"", "makerare": "\"true\"", "minabund": "\"0\"", "keepties": "\"true\"", "label": "null", "dbkey": "\"hg17\"", "groups": "null", "minnumsamples": "\"0\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "minpercent": "\"0\"", "minpercentsamples": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16884", "id": "1475351371259894", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_filter_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"minabund": "1", "otu": {"src": "hda", "id": "3b15c7f26dc0569d"}, "groups": ["forest", "pasture"], "label": ["0.05", "0.29", "0.33"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "3b15c7f26dc0569d", "uuid": "5fb0d6d8-3073-4326-a70a-191ff53c54aa"}}, "update_time": "2018-02-08T17:25:18.973667", "tool_id": "mothur_filter_shared", "outputs": {"__new_primary_file_0.33|0.29__": {"src": "hda", "id": "6535d25f5d400f01", "uuid": "8e5e98b5-ad5e-42e7-85f6-e1460da8e9e1"}, "__new_primary_file_0.33|0.05__": {"src": "hda", "id": "ef11ae9dd5e1ab5d", "uuid": "247b8f50-45f4-4926-955a-c6c15494ecf3"}, "logfile": {"src": "hda", "id": "4065036011f723eb", "uuid": "6b0186d1-9972-485c-b3b4-4c252d55df05"}, "__new_primary_file_0.33|0.33__": {"src": "hda", "id": "72b2b39740f9703c", "uuid": "07092db3-77f7-4bf4-ac2b-167b728f30d0"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > filter.shared(shared=otu.dat,label=0.05-0.29-0.33,groups=forest-pasture \r,minabund=1,minpercent=0,rarepercent=0,keepties=true,minnumsamples=0,minpercents \ramples=0,mintotal=0,makerare=true)\n0.05\n\nRemoved 71 OTUs.\n0.29\n\nRemoved 5 OTUs.\n0.33\n\nRemoved 4 OTUs.\n\nOutput File Names: \notu.0.05.filter.dat\notu.0.29.filter.dat\notu.0.33.filter.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_813.dat' otu.dat &&  echo 'filter.shared( shared=otu.dat, label=0.05-0.29-0.33, groups=forest-pasture, minabund=1, minpercent=0, rarepercent=0, keepties=true, minnumsamples=0, minpercentsamples=0, mintotal=0, makerare=true )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:25:15.440162", "params": {"rarepercent": "\"0\"", "mintotal": "\"0\"", "makerare": "\"true\"", "minabund": "\"1\"", "keepties": "\"true\"", "label": "[\"0.05\", \"0.29\", \"0.33\"]", "dbkey": "\"hg17\"", "groups": "[\"forest\", \"pasture\"]", "minnumsamples": "\"0\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "minpercent": "\"0\"", "minpercentsamples": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "16968", "id": "8c2787e62639209d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_filter_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "da36c3eb2b3d65a2"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "da36c3eb2b3d65a2", "uuid": "cba3d5fe-09fc-4e04-91ab-7bbc05d36321"}}, "update_time": "2018-02-08T17:25:37.273222", "tool_id": "mothur_get_communitytype", "outputs": {"__new_primary_file_1.dmm.5.mix|1.dmm.2.mix__": {"src": "hda", "id": "46d9987333936090", "uuid": "b0623781-62e3-4150-ac7f-239be4a71b70"}, "parameters": {"src": "hda", "id": "dd4d919ea4ea0b29", "uuid": "d612eb45-53ea-47b8-95d4-873e5618fb69"}, "fit": {"src": "hda", "id": "e3f91a060b9b80d1", "uuid": "6a770929-dc86-4bc0-8900-c47fd74aaf88"}, "__new_primary_file_1.dmm.5.mix|1.dmm.4.mix__": {"src": "hda", "id": "80bd938d1e1607e1", "uuid": "1235a90e-f5b0-48e0-8831-411fc5e6dd2f"}, "__new_primary_file_1.dmm.5.mix|1.dmm.3.mix__": {"src": "hda", "id": "9140d1ef204facd8", "uuid": "1bf8cde3-d372-4fb5-b7e1-177508ce896f"}, "summary": {"src": "hda", "id": "45ca4a044ef44e98", "uuid": "51c92525-d990-4b94-aeb0-5f4b88275daf"}, "__new_primary_file_1.dmm.5.mix|1.dmm.5.mix__": {"src": "hda", "id": "fd784843823fdc6f", "uuid": "aad19a5d-9410-4cff-8b9a-20900d8dc2b7"}, "design": {"src": "hda", "id": "1fb72aa777fd09ee", "uuid": "3509ad1e-3446-40e3-aec1-788fa6b63e6d"}, "logfile": {"src": "hda", "id": "957ab5f6bc45f41a", "uuid": "8648dd7f-d3e4-45d9-974a-511fb5a40d0b"}, "__new_primary_file_1.dmm.5.mix|1.dmm.1.mix__": {"src": "hda", "id": "512bef0a5c0a6baf", "uuid": "fdc4d9b4-eca5-4859-ace7-6cb87f40b831"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.communitytype(shared=shared.dat,method=dmm,minpartitions=5,maxparti \rtions=10,optimizegap=3,processors=1)\nUsing 1 processor\n1\nK\tNLE\t\tlogDet\tBIC\t\tAIC\t\tLaplace\n1\t1216.81\t81.07\t1265.15\t1260.81\t1216.91\n2\t1277.35\t93.64\t1375.12\t1366.35\t1242.39\n3\t1394.29\t95.07\t1541.51\t1528.29\t1318.69\n4\t1506.74\t56.14\t1703.39\t1685.74\t1370.32\n5\t1609.90\t33.23\t1855.99\t1833.90\t1420.67\n\nOutput File Names: \nshared.1.dmm.mix.fit\nshared.1.dmm.1.mix.posterior\nshared.1.dmm.1.mix.relabund\nshared.1.dmm.2.mix.posterior\nshared.1.dmm.2.mix.relabund\nshared.1.dmm.3.mix.posterior\nshared.1.dmm.3.mix.relabund\nshared.1.dmm.4.mix.posterior\nshared.1.dmm.4.mix.relabund\nshared.1.dmm.5.mix.posterior\nshared.1.dmm.5.mix.relabund\nshared.1.dmm.mix.design\nshared.1.dmm.mix.parameters\nshared.1.dmm.mix.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_818.dat' shared.dat &&  echo 'get.communitytype( shared=shared.dat, method=dmm, minpartitions=5, maxpartitions=10, optimizegap=3, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:25:32.972501", "params": {"optimizegap": "\"3\"", "m": "{\"method\": \"dmm\", \"__current_case__\": 0}", "dbkey": "\"hg17\"", "label": "null", "subsample": "\"-1\"", "minpartitions": "\"5\"", "groups": "null", "maxpartitions": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17059", "id": "1347e273f5270371", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_communitytype.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"m|method": "kmeans", "label": "1", "subsample": "0", "groups": ["F003D000", "F003D002", "F003D006", "F003D008", "F003D142"], "m|iters": "100", "maxpartitions": "4", "otu": {"src": "hda", "id": "fa032b562e153122"}, "m|calc": "manhattan"}, "job": {"inputs": {"otu": {"src": "hda", "id": "fa032b562e153122", "uuid": "5bfd8e93-46fe-453c-a4da-48ec58a85d3e"}}, "update_time": "2018-02-08T17:26:23.046397", "tool_id": "mothur_get_communitytype", "outputs": {"__new_primary_file_1.kmeans.4.mix|1.kmeans.1.mix__": {"src": "hda", "id": "d094c18f3f0c4217", "uuid": "84368f6d-4d9c-4113-9bd6-257309aed486"}, "__new_primary_file_1.kmeans.4.mix|1.kmeans.4.mix__": {"src": "hda", "id": "af3fae2a84d45574", "uuid": "c2b87b12-c748-4afe-8fe5-c6df9b709939"}, "fit": {"src": "hda", "id": "b1d26ebda0776d51", "uuid": "58f10d11-2ccf-4f31-a25c-de3108ef4496"}, "__new_primary_file_1.kmeans.4.mix|1.kmeans.2.mix__": {"src": "hda", "id": "5498b8b462f50992", "uuid": "1248da22-bd19-4fd6-ad84-b8bb15632ed6"}, "__new_primary_file_1.kmeans.4.mix|1.kmeans.3.mix__": {"src": "hda", "id": "172394607370a660", "uuid": "31f888f5-2ccb-4958-a217-4eac5900c86e"}, "design": {"src": "hda", "id": "c1aa962b6790390b", "uuid": "a10310a9-90b9-4c09-9d30-bc836823e2d4"}, "logfile": {"src": "hda", "id": "8d9b160acaa0feca", "uuid": "d19c3919-9eb7-4dac-a914-7c053983d7b3"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.communitytype(shared=shared.dat,label=1,groups=F003D000-F003D002-F0 \r03D006-F003D008-F003D142,method=kmeans,calc=manhattan,iters=100,subsample=T,minp \rartitions=5,maxpartitions=4,optimizegap=3,processors=1)\nUsing 1 processor\n1\nK\tCH\tF003D000\tF003D002\tF003D006\tF003D008\tF003D142\n100\n1\t0.000000\t0.000000\t0.000000\t0.000000\t0.000000\t0.000000\n2\t4.168014\t0.296084\t0.201078\t0.496841\t0.122851\t0.606822\n3\t0.646053\t-0.138889\t0.000000\t0.399794\t-0.239057\t0.594163\n4\t0.182272\t-0.138889\t0.000000\t0.000000\t-0.239057\t0.000000\n\nOutput File Names: \nshared.1.kmeans.mix.fit\nshared.1.kmeans.1.mix.posterior\nshared.1.kmeans.1.mix.relabund\nshared.1.kmeans.2.mix.posterior\nshared.1.kmeans.2.mix.relabund\nshared.1.kmeans.3.mix.posterior\nshared.1.kmeans.3.mix.relabund\nshared.1.kmeans.4.mix.posterior\nshared.1.kmeans.4.mix.relabund\nshared.1.kmeans.mix.design\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_834.dat' shared.dat &&  echo 'get.communitytype( shared=shared.dat, label=1, groups=F003D000-F003D002-F003D006-F003D008-F003D142, method=kmeans, calc=manhattan, iters=100, subsample=T, minpartitions=5, maxpartitions=4, optimizegap=3, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:26:19.082655", "params": {"optimizegap": "\"3\"", "m": "{\"iters\": \"100\", \"calc\": \"manhattan\", \"method\": \"kmeans\", \"__current_case__\": 1}", "dbkey": "\"hg17\"", "label": "\"1\"", "subsample": "\"0\"", "minpartitions": "\"5\"", "groups": "[\"F003D000\", \"F003D002\", \"F003D006\", \"F003D008\", \"F003D142\"]", "maxpartitions": "\"4\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17158", "id": "4ffe0c6ec86fa835", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_communitytype.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "b7e286a9dc222a5c"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "b7e286a9dc222a5c", "uuid": "bdec2f8f-1198-44cc-b57e-a04799d0e832"}}, "update_time": "2018-02-08T17:26:59.775503", "tool_id": "mothur_get_coremicrobiome", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "a6d2cc1cc42ebc8f", "uuid": "233065b3-98ac-4c29-b30e-3b306f62aff7"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "2359309399418ebc", "uuid": "d78b6caa-de9d-4319-ada9-88432db48511"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "075a237cd5260f96", "uuid": "4f8c8914-582b-4740-b421-c7e4d86ec21e"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "ec7711f2346cbca2", "uuid": "654e2c05-b90c-4435-860a-97156d892f09"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "793e3e9c6f59a42d", "uuid": "3fc8cb23-3378-4f70-9b14-ee4904c6fff6"}, "__new_primary_file_unique|0.16__": {"src": "hda", "id": "b870f50c8df3ba43", "uuid": "be1c738a-4a78-48d2-97cf-739fb8a700cf"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "464c0ed74865d74c", "uuid": "8171f1de-f71d-42a8-a7e3-447b4be12d61"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "1000d2466fcfad34", "uuid": "736b8b91-4f88-4616-9c7e-d0a27458847f"}, "__new_primary_file_unique|0.15__": {"src": "hda", "id": "fbe5f3e3e3e03570", "uuid": "c79935f9-a980-4a16-8ee1-734ad89f89d1"}, "__new_primary_file_unique|0.08__": {"src": "hda", "id": "dd222fd69f0dcf77", "uuid": "593ab8a8-e41a-467f-9e5f-73864cc64489"}, "__new_primary_file_unique|0.14__": {"src": "hda", "id": "ff8b3978bcf080b9", "uuid": "634b157a-6818-4084-bb17-2a5e387c40f2"}, "__new_primary_file_unique|0.13__": {"src": "hda", "id": "9f2ff1f2038a0454", "uuid": "078e742d-b87a-413f-aaaf-a67611bc6951"}, "__new_primary_file_unique|0.09__": {"src": "hda", "id": "3d4c423d57259fbe", "uuid": "2985e026-f0ee-41dc-9889-62be13ea052f"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "aeb3a7d27531d8af", "uuid": "ad4e98b4-c643-4d4a-a391-e2b966da62aa"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "306d83d29e038396", "uuid": "6f9746f6-d36b-425a-bf6b-960f1f3e2b66"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "1bdec2d5353dc7ac", "uuid": "ab5376c5-c51d-4ef7-b34f-e9f1e8d7fa48"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "753f526c4fe64c6a", "uuid": "1d767ed6-fed9-4555-86b8-b7e57cb0ecff"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "0e57173360853a16", "uuid": "c68d169e-4ce1-4884-97e3-74695ade4348"}, "__new_primary_file_unique|0.25__": {"src": "hda", "id": "6d4181f50c48e719", "uuid": "224c4143-b35f-41ec-ac34-4d49db58eeed"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "39aace9ebf1f79e7", "uuid": "dff73c25-fa2e-4d9d-bbba-c5bb39012224"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "9009f3fbd6374ed9", "uuid": "62b406ba-bcea-487a-befd-2df70395590b"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "e5cb57ff5e9a2036", "uuid": "142511d9-525c-4498-8b73-e6d5a6af8882"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "3a712f92b35e894a", "uuid": "39100123-be01-44f0-a652-52508139227c"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "ab53f78f19a8abb1", "uuid": "51d68092-e60d-400c-bf47-d6dd75569dba"}, "logfile": {"src": "hda", "id": "7bfed31e5ec18c3b", "uuid": "2d37f2f3-9ea3-4c56-babd-56e719ca5cad"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "a015212d4be18feb", "uuid": "ece7a697-24a6-42bc-a04c-2567edc4f37d"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "06d05dea0c9ced7b", "uuid": "74c220de-4196-497d-9a83-497883ef5336"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "c26638b7e7264d47", "uuid": "2a4a43d5-d028-44c6-9e80-401e0c943d70"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "cfd269e45b767b10", "uuid": "91742f4b-eca2-4b50-b0dd-f58a9bb2ea12"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "86305fdc0e529488", "uuid": "295d95a4-8e81-45c9-ba14-9df0fbc7a735"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "fd5c24c1cb65fd09", "uuid": "60e02f42-5541-40b7-ad8d-6a799983f01f"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "d0db08ce3cbc8382", "uuid": "f25a63c1-78e3-4655-86f4-e58b5b012e51"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "e2424d83ba170c8a", "uuid": "d0bb553a-75f1-4097-8a16-9b50032c5694"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "90ebacaedc3e1f42", "uuid": "0c90a057-a0f3-4382-a45b-8838caa3515b"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "2d9271a917bcfaf1", "uuid": "d2bee9b2-9f4e-4c58-b86a-07de1c2a2779"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "b13eb5b1dace709b", "uuid": "6f9bf0fa-95a7-44db-ae7d-0f44bf126dbc"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "fd9f0efd7554e81c", "uuid": "94481846-0b13-4170-b7b2-e96063435573"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.coremicrobiome(shared=otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.core.microbiome\notu.0.01.core.microbiome\notu.0.02.core.microbiome\notu.0.03.core.microbiome\notu.0.04.core.microbiome\notu.0.05.core.microbiome\notu.0.06.core.microbiome\notu.0.07.core.microbiome\notu.0.08.core.microbiome\notu.0.09.core.microbiome\notu.0.10.core.microbiome\notu.0.11.core.microbiome\notu.0.12.core.microbiome\notu.0.13.core.microbiome\notu.0.14.core.microbiome\notu.0.15.core.microbiome\notu.0.16.core.microbiome\notu.0.17.core.microbiome\notu.0.18.core.microbiome\notu.0.19.core.microbiome\notu.0.20.core.microbiome\notu.0.21.core.microbiome\notu.0.22.core.microbiome\notu.0.23.core.microbiome\notu.0.24.core.microbiome\notu.0.25.core.microbiome\notu.0.26.core.microbiome\notu.0.27.core.microbiome\notu.0.29.core.microbiome\notu.0.32.core.microbiome\notu.0.33.core.microbiome\notu.0.36.core.microbiome\notu.0.38.core.microbiome\notu.0.41.core.microbiome\notu.0.45.core.microbiome\notu.0.55.core.microbiome\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_846.dat' otu.dat &&  echo 'get.coremicrobiome( shared=otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:26:55.029493", "params": {"abundance": "\"\"", "samples": "\"\"", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "output": "\"fraction\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17250", "id": "6fb508dbe1736155", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_coremicrobiome.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"abundance": "30", "otu": {"src": "hda", "id": "58c9e52c4a64b228"}, "label": ["0.05", "0.22", "0.45"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "58c9e52c4a64b228", "uuid": "8ce00b7a-a8a2-430e-8bc6-84d7fbd2a3bf"}}, "update_time": "2018-02-08T17:27:19.754618", "tool_id": "mothur_get_coremicrobiome", "outputs": {"__new_primary_file_0.45|0.22__": {"src": "hda", "id": "afce6c63a9e7aea5", "uuid": "1845c435-5d48-4b12-b043-c80f08244f67"}, "logfile": {"src": "hda", "id": "c09e2ca1f1e4cd99", "uuid": "082703a5-d021-4379-b991-d1c9af2b43c6"}, "__new_primary_file_0.45|0.45__": {"src": "hda", "id": "9c87d501351cb89f", "uuid": "f88274c8-a2e6-41b8-849b-9f24bc40bdaf"}, "__new_primary_file_0.45|0.05__": {"src": "hda", "id": "816dd7bcb4c0fa93", "uuid": "60ee11c0-8707-40a1-afb8-324a92eecba5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.coremicrobiome(shared=otu.dat,label=0.05-0.22-0.45,abundance=30)\n0.05\n0.22\n0.45\n\nOutput File Names: \notu.0.05.core.microbiome\notu.0.05.core.microbiomelist\notu.0.22.core.microbiome\notu.0.22.core.microbiomelist\notu.0.45.core.microbiome\notu.0.45.core.microbiomelist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_884.dat' otu.dat &&  echo 'get.coremicrobiome( shared=otu.dat ,label=0.05-0.22-0.45 ,abundance=30 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:27:16.293030", "params": {"abundance": "\"30\"", "samples": "\"\"", "dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.22\", \"0.45\"]", "groups": "null", "output": "\"fraction\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17337", "id": "38f13aa9fc15acbf", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_coremicrobiome.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input|dist": {"src": "hda", "id": "da06cbb007a4cb61"}, "input|source": "phylip", "accnos": {"src": "hda", "id": "0126412added8c8e"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "0126412added8c8e", "uuid": "c191f3eb-cc95-4db0-9524-2f70d2b5e647"}, "dist": {"src": "hda", "id": "da06cbb007a4cb61", "uuid": "b1ed6156-408c-4f43-80fc-5536243e55e7"}}, "update_time": "2018-02-08T17:27:48.325338", "tool_id": "mothur_get_dists", "outputs": {"logfile": {"src": "hda", "id": "b3cba6951cf833ad", "uuid": "9013f911-7f16-4fbe-b982-75d3c13d2ab8"}, "pick_dist": {"src": "hda", "id": "26507515799dee2a", "uuid": "e3b28f5f-eb02-4fe6-bdd2-7b45e1539df4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.dists(accnos=accnos.dat,phylip=input.dist.dat)\nSelected 8 groups or sequences from your phylip file.\n\nOutput File names: \ninput.dist.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_893.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_892.dat' input.dist.dat &&  echo 'get.dists( accnos=accnos.dat, phylip=input.dist.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:27:45.313518", "params": {"input": "{\"source\": \"phylip\", \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 892}]}, \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17452", "id": "3ecde483422ba55d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_dists.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"shared": {"src": "hda", "id": "b792db3724607288"}}, "job": {"inputs": {"shared": {"src": "hda", "id": "b792db3724607288", "uuid": "ee9810f6-620b-469e-939d-54f8b55afc92"}}, "update_time": "2018-02-08T17:28:05.694410", "tool_id": "mothur_get_group", "outputs": {"bootgroups": {"src": "hda", "id": "f9be15f92a6fe6ec", "uuid": "5c5c9da1-3a70-476f-bef4-df34961637b2"}, "logfile": {"src": "hda", "id": "668671b8705dc162", "uuid": "0a519a4e-a481-4c50-bfea-ab7139416da0"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.group(shared=shared.dat)\nforest\npasture\n\nOutput File Names: \n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_896.dat' shared.dat &&  echo 'get.group( shared=shared.dat )' | sed 's/ //g' | mothur | tee mothur.out.log &&  cat mothur.*.logfile | head -n-6 | sed '1,30d' > \"/tmp/saskia/tmpKSDp0p/files/000/dataset_898.dat\"", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:28:02.572268", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17539", "id": "6776b4c51106726f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_group.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"group_in": {"src": "hda", "id": "847f267ec407e762"}, "groupnames|groups": ["forest", "pasture"], "groupnames|source": "groups"}, "job": {"inputs": {"group_in": {"src": "hda", "id": "847f267ec407e762", "uuid": "52ca1b29-6082-4531-bade-d86f51e9f447"}}, "update_time": "2018-02-08T17:28:18.288203", "tool_id": "mothur_get_groups", "outputs": {"group_out": {"src": "hda", "id": "4561df7fd732de3f", "uuid": "3cda55f1-262a-4201-b49a-9e0c022a36e4"}, "logfile": {"src": "hda", "id": "aab4e8dd7c444bc2", "uuid": "4a0646f7-9b7f-472f-8bdd-7af6a790339d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.groups(group=group_in.dat,groups=forest-pasture)\nSelected 98 sequences from your group file.\n\nOutput File names: \ngroup_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_899.dat' group_in.dat && ln -s 'None' fasta_in.dat && ln -s 'None' name_in.dat && ln -s 'None' list_in.dat && ln -s 'None' shared_in.dat && ln -s 'None' taxonomy_in.dat && ln -s 'None' design_in.dat &&  echo 'get.groups( group=group_in.dat ,groups=forest-pasture )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:28:15.314231", "params": {"design_in": "null", "shared_in": "null", "fasta_in": "null", "dbkey": "\"hg17\"", "groupnames": "{\"source\": \"groups\", \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 0}", "taxonomy_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17626", "id": "7e438c048dc73282", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_groups.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"group_in": {"src": "hda", "id": "0650f1de48127da2"}, "groupnames|accnos": {"src": "hda", "id": "a614724d012c5b21"}, "groupnames|source": "accnos"}, "job": {"inputs": {"group_in": {"src": "hda", "id": "0650f1de48127da2", "uuid": "fd50498c-4bc4-4221-9e90-73e70d2a37ad"}, "accnos": {"src": "hda", "id": "a614724d012c5b21", "uuid": "e4dab025-9ff2-4b5a-81fb-f5519760b90d"}}, "update_time": "2018-02-08T17:28:38.840237", "tool_id": "mothur_get_groups", "outputs": {"group_out": {"src": "hda", "id": "4420605beb7b8bfb", "uuid": "2cd9f556-01d6-4537-b6a4-cfb46c181f17"}, "logfile": {"src": "hda", "id": "5bea13ccc5be4601", "uuid": "54f9eb15-cd81-4161-abe4-6a5298ccc88e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.groups(group=group_in.dat,accnos=groupnames.accnos.dat)\nSelected 98 sequences from your group file.\n\nOutput File names: \ngroup_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_902.dat' group_in.dat && ln -s 'None' fasta_in.dat && ln -s 'None' name_in.dat && ln -s 'None' list_in.dat && ln -s 'None' shared_in.dat && ln -s 'None' taxonomy_in.dat && ln -s 'None' design_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_903.dat' groupnames.accnos.dat &&  echo 'get.groups( group=group_in.dat ,accnos=groupnames.accnos.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:28:35.903967", "params": {"design_in": "null", "shared_in": "null", "fasta_in": "null", "dbkey": "\"hg17\"", "groupnames": "{\"source\": \"accnos\", \"accnos\": {\"values\": [{\"src\": \"hda\", \"id\": 903}]}, \"__current_case__\": 1}", "taxonomy_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17749", "id": "daf78d18ceb29125", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_groups.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"shared_in": {"src": "hda", "id": "d67967a926798f5f"}, "fasta_in": {"src": "hda", "id": "35283c805171c447"}, "list_in": {"src": "hda", "id": "f607da3436fbec2f"}, "group_in": {"src": "hda", "id": "2678f705a638379e"}, "groupnames|source": "accnos", "groupnames|accnos": {"src": "hda", "id": "0cb926f24836ac7c"}, "name_in": {"src": "hda", "id": "cfe031a04a60c053"}}, "job": {"inputs": {"shared_in": {"src": "hda", "id": "d67967a926798f5f", "uuid": "51ef0239-4c60-46ca-968b-309399b500fe"}, "fasta_in": {"src": "hda", "id": "35283c805171c447", "uuid": "57d4d1b8-7ada-432f-9f75-b44c0176ba84"}, "group_in": {"src": "hda", "id": "2678f705a638379e", "uuid": "123b585d-dd83-4d4d-ad63-a21cca9786c2"}, "accnos": {"src": "hda", "id": "0cb926f24836ac7c", "uuid": "12c17915-dd32-45eb-a48a-2f7302e6b71f"}, "list_in": {"src": "hda", "id": "f607da3436fbec2f", "uuid": "642ba2bd-7ef7-491e-b46b-89ad138d6c91"}, "name_in": {"src": "hda", "id": "cfe031a04a60c053", "uuid": "7dadd403-a404-4254-8947-6231ad67f1d4"}}, "update_time": "2018-02-08T17:29:19.880133", "tool_id": "mothur_get_groups", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "e7b2fbcbe0130dc5", "uuid": "0fc85bad-a4cd-487b-9d9e-917735e5f337"}, "fasta_out": {"src": "hda", "id": "e3d34fd694cc8229", "uuid": "df83ec03-d83a-471f-9667-05c4c355b36d"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "49e0d2540b109fa1", "uuid": "0512e81e-973d-4e2c-b6aa-76f587ab07ae"}, "name_out": {"src": "hda", "id": "dc3d09c4b8e0106b", "uuid": "e2ef3817-ebec-4af6-9523-3162b6396cf0"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "28f4914f81d01a57", "uuid": "11bd60dd-fb43-41f9-a092-217e04111f0f"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "0c74b38aee0a0707", "uuid": "e22ad6ae-070b-4a3c-bf25-aa64d1b9ed46"}, "__new_primary_file_unique|0.16__": {"src": "hda", "id": "d81fd9932dcc170a", "uuid": "041d0e7f-db5b-44eb-9fea-dcf4b2fb87c7"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "69399224f9256324", "uuid": "2ce57bef-5a87-49c8-9fb0-d8875771706a"}, "__new_primary_file_unique|0.25__": {"src": "hda", "id": "f0a1b060065d5446", "uuid": "6cc32651-11ef-4e7f-9f83-92e41535b9a2"}, "__new_primary_file_unique|0.15__": {"src": "hda", "id": "59577937f74245aa", "uuid": "8495987e-d861-4ba0-b99d-336fddc547e1"}, "__new_primary_file_unique|0.08__": {"src": "hda", "id": "2b396abc964fbea2", "uuid": "8978e23d-4166-47e6-b9b2-5752815535b6"}, "__new_primary_file_unique|0.14__": {"src": "hda", "id": "f21afe41a9b1581c", "uuid": "dc1d3cba-9e86-4969-9b92-b9a176495360"}, "__new_primary_file_unique|0.13__": {"src": "hda", "id": "1ed3e70d24b98524", "uuid": "45b7a913-f48a-43d0-a013-afddb51f8ea6"}, "__new_primary_file_unique|0.09__": {"src": "hda", "id": "1fd6dc2cbb454726", "uuid": "17866495-61a1-4938-a035-15962d8ab6d0"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "64114e2b118e5c93", "uuid": "5f3900a8-63e5-4c6d-b6fa-37f6c4e5cf66"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "0edc42988cb29650", "uuid": "6db90c67-7578-49e9-b756-d816a9106382"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "ba68b57cc8005e59", "uuid": "789ba415-6a47-4be9-a6b7-5dfd4b42ceec"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "00df4bed4eb73805", "uuid": "80186821-a510-4bcb-8006-c6b0c41c193c"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "63acbb87262a1307", "uuid": "0b55ba95-3740-4d53-bd41-150e5b5fc8dd"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "5c0d4def21b0cc81", "uuid": "aa6c782c-87a3-4853-b401-b017615f4c6f"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "835154436814778d", "uuid": "09dc6d61-399d-4a0e-b140-77741c901fef"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "55898ade0931da26", "uuid": "b06b0390-f7d6-4ade-b33d-daa143835a10"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "d10947b9879b82b2", "uuid": "c1bee6d0-b738-4568-9372-7ae85bdc2952"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "d30ef2c42df90932", "uuid": "1c58dab4-07f1-459a-aadb-6708836de56e"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "8b5aaaded4e2744a", "uuid": "ddd0691d-4c4a-480e-b33c-682dec6fd1a9"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "e4bf668168cf4d28", "uuid": "f61f63c3-eb97-4c8f-b84f-f83c84fc7029"}, "logfile": {"src": "hda", "id": "9991dcf0fd7f0858", "uuid": "f8771e9a-bf6e-416a-b94f-daff5d8d95d6"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "6106d47609a22f86", "uuid": "2afdba2a-cc11-4655-9ccc-b744a34bff5f"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "7ebdd79957123fd3", "uuid": "938d5e9a-2fdb-40fa-b33b-e4214fb89732"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "884d04d1bc49fbdb", "uuid": "a592c21e-ecf3-4904-9e4e-e737b0745087"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "498289f2374aaabc", "uuid": "2d5e7e5f-eb29-4c83-8ee2-76e8c2b04364"}, "group_out": {"src": "hda", "id": "f5bbc78947a4eedf", "uuid": "9d342395-a884-438a-a94a-869933812708"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "9b47053a34d461cf", "uuid": "bbfa83f3-3cf1-4a5a-8203-45444602993e"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "de60620e584e5f58", "uuid": "5934793a-5722-4ed0-a76d-002a7dc64b89"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "9d84a8c0f8b83109", "uuid": "6b911bb6-5197-49a3-a901-25346bf3ac3c"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "c2a06a3a7a66a110", "uuid": "57f7b1b4-b2f9-4724-b60b-48b5474918d6"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "e6fa111c52a4ac04", "uuid": "3d9d4e51-96cc-46e0-a698-edc16d5368ea"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "27741565111063db", "uuid": "4e53bb98-a46f-4c49-af70-69c408fadbd6"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "0bc7636427d365b6", "uuid": "473f7936-2596-4bf1-9ca1-07604f66f8a3"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "db7df1b0dd9c9f66", "uuid": "eaa9fc5a-aecb-45fc-abc5-3c51a2ea1257"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.groups(group=group_in.dat,accnos=groupnames.accnos.dat,fasta=fasta_ \rin.dat,name=name_in.dat,list=list_in.dat,shared=shared_in.dat)\nSelected 98 sequences from your name file.\nSelected 98 sequences from your fasta file.\nSelected 98 sequences from your group file.\nSelected 98 sequences from your list file.\nSelected groups: forest, pasture from your shared file.\n\nOutput File names: \nname_in.pick.dat\nfasta_in.pick.dat\ngroup_in.pick.dat\nlist_in.unique.pick.dat\nlist_in.0.01.pick.dat\nlist_in.0.02.pick.dat\nlist_in.0.03.pick.dat\nlist_in.0.04.pick.dat\nlist_in.0.05.pick.dat\nlist_in.0.06.pick.dat\nlist_in.0.07.pick.dat\nlist_in.0.08.pick.dat\nlist_in.0.09.pick.dat\nlist_in.0.10.pick.dat\nlist_in.0.11.pick.dat\nlist_in.0.12.pick.dat\nlist_in.0.13.pick.dat\nlist_in.0.14.pick.dat\nlist_in.0.15.pick.dat\nlist_in.0.16.pick.dat\nlist_in.0.17.pick.dat\nlist_in.0.18.pick.dat\nlist_in.0.19.pick.dat\nlist_in.0.20.pick.dat\nlist_in.0.21.pick.dat\nlist_in.0.22.pick.dat\nlist_in.0.23.pick.dat\nlist_in.0.24.pick.dat\nlist_in.0.25.pick.dat\nlist_in.0.26.pick.dat\nlist_in.0.27.pick.dat\nlist_in.0.29.pick.dat\nlist_in.0.32.pick.dat\nlist_in.0.33.pick.dat\nlist_in.0.36.pick.dat\nlist_in.0.38.pick.dat\nlist_in.0.41.pick.dat\nlist_in.0.45.pick.dat\nlist_in.0.55.pick.dat\nshared_in.unique.pick.dat\nshared_in.0.01.pick.dat\nshared_in.0.02.pick.dat\nshared_in.0.03.pick.dat\nshared_in.0.04.pick.dat\nshared_in.0.05.pick.dat\nshared_in.0.06.pick.dat\nshared_in.0.07.pick.dat\nshared_in.0.08.pick.dat\nshared_in.0.09.pick.dat\nshared_in.0.10.pick.dat\nshared_in.0.11.pick.dat\nshared_in.0.12.pick.dat\nshared_in.0.13.pick.dat\nshared_in.0.14.pick.dat\nshared_in.0.15.pick.dat\nshared_in.0.16.pick.dat\nshared_in.0.17.pick.dat\nshared_in.0.18.pick.dat\nshared_in.0.19.pick.dat\nshared_in.0.20.pick.dat\nshared_in.0.21.pick.dat\nshared_in.0.22.pick.dat\nshared_in.0.23.pick.dat\nshared_in.0.24.pick.dat\nshared_in.0.25.pick.dat\nshared_in.0.26.pick.dat\nshared_in.0.27.pick.dat\nshared_in.0.29.pick.dat\nshared_in.0.32.pick.dat\nshared_in.0.33.pick.dat\nshared_in.0.36.pick.dat\nshared_in.0.38.pick.dat\nshared_in.0.41.pick.dat\nshared_in.0.45.pick.dat\nshared_in.0.55.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_906.dat' group_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_908.dat' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_909.dat' name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_910.dat' list_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_911.dat' shared_in.dat && ln -s 'None' taxonomy_in.dat && ln -s 'None' design_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_907.dat' groupnames.accnos.dat &&  echo 'get.groups( group=group_in.dat ,accnos=groupnames.accnos.dat ,fasta=fasta_in.dat ,name=name_in.dat ,list=list_in.dat ,shared=shared_in.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:29:09.781970", "params": {"design_in": "null", "taxonomy_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groupnames": "{\"source\": \"accnos\", \"accnos\": {\"values\": [{\"src\": \"hda\", \"id\": 907}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "17947", "id": "cda64434023ac031", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_groups.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "57529f16d280395b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "57529f16d280395b", "uuid": "32739e7b-3636-46fd-b3ac-cea446510cfb"}}, "update_time": "2018-02-08T17:30:01.971982", "tool_id": "mothur_get_label", "outputs": {"logfile": {"src": "hda", "id": "bc9fca4354129cac", "uuid": "067bdef1-3a84-4829-8c96-a48e32186d48"}, "labels_list": {"src": "hda", "id": "201e02e237ed0c72", "uuid": "4ba5be37-6f34-4c01-8556-825aa312902f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.label(sabund=otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_988.dat' otu.dat &&  echo 'get.label( sabund=otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log &&  cat mothur.*.logfile | head -n-3 | sed '1,30d' > '/tmp/saskia/tmpKSDp0p/files/000/dataset_990.dat'", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:29:58.831218", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18052", "id": "e038b12fcc34712c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_label.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "49cb3d1841241873"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "49cb3d1841241873", "uuid": "3a2bc5f4-1e07-46cd-a0be-4cca2b665959"}}, "update_time": "2018-02-08T17:30:19.631582", "tool_id": "mothur_get_label", "outputs": {"logfile": {"src": "hda", "id": "ba98875ce3cc6214", "uuid": "f9116359-0d6b-4f41-b691-665ce1d3a1a7"}, "labels_list": {"src": "hda", "id": "ca6dcdef942ee1ff", "uuid": "8263f4f7-7637-44d9-8018-af63e1aaa888"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.label(rabund=otu.dat)\n0.03\n0.05\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_991.dat' otu.dat &&  echo 'get.label( rabund=otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log &&  cat mothur.*.logfile | head -n-3 | sed '1,30d' > '/tmp/saskia/tmpKSDp0p/files/000/dataset_993.dat'", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:30:16.297205", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18142", "id": "57d21b82f66bdde1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_label.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "8c90b885b85c197b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "8c90b885b85c197b", "uuid": "14ef5623-7a0b-48ec-a0f1-b67dfcf3c3df"}}, "update_time": "2018-02-08T17:30:37.243891", "tool_id": "mothur_get_label", "outputs": {"logfile": {"src": "hda", "id": "d0915a2b5dcfc5c8", "uuid": "4f7aa13b-d0c7-447d-b1ac-d33bfe1cd0c1"}, "labels_list": {"src": "hda", "id": "d63ffe6d4f3dca3c", "uuid": "7e207c4c-5c60-4eb8-9b35-7c17721e16b6"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.label(list=otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_994.dat' otu.dat &&  echo 'get.label( list=otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log &&  cat mothur.*.logfile | head -n-3 | sed '1,30d' > '/tmp/saskia/tmpKSDp0p/files/000/dataset_996.dat'", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:30:34.086402", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18244", "id": "b76e2c1d909ec95b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_label.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"file|taxonomy": {"src": "hda", "id": "e42f3afaf409615c"}, "file|filetype": "usetaxonomy", "taxon": "Bacteria;Firmicutes;"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "e42f3afaf409615c", "uuid": "e7dc8e71-b2d3-4775-aac9-a05c3db431de"}}, "update_time": "2018-02-08T17:30:54.719853", "tool_id": "mothur_get_lineage", "outputs": {"logfile": {"src": "hda", "id": "7ea54b244028000c", "uuid": "54d577a5-2051-4705-a621-041d2df19088"}, "taxonomy_out": {"src": "hda", "id": "370469ee2a7f9bfc", "uuid": "2d258268-f5c1-4efa-a6cd-1640a8072a07"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.lineage(taxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/000/dataset_997.dat' file.taxonomy.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat &&  echo 'get.lineage( taxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;'\"' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:30:51.569064", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"Bacteria;Firmicutes;\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 997}]}, \"filetype\": \"usetaxonomy\", \"taxons\": null, \"__current_case__\": 0}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18333", "id": "6cafac5eedb91caf", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_lineage.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta_in": {"src": "hda", "id": "9430897aec45eb57"}, "taxon": "Bacteria;Firmicutes;,Bacteria;Actinobacteria;", "list_in": {"src": "hda", "id": "c9e1a49c1225960d"}, "group_in": {"src": "hda", "id": "842c471bdfd9c887"}, "file|taxonomy": {"src": "hda", "id": "8e944aefd2c834c6"}, "alignreport_in": {"src": "hda", "id": "11a8d37cccceb071"}, "file|filetype": "usetaxonomy", "name_in": {"src": "hda", "id": "70c3e648e0bbdb1c"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "8e944aefd2c834c6", "uuid": "7c0d62a8-03c2-4142-8222-f461f4e3f089"}, "fasta_in": {"src": "hda", "id": "9430897aec45eb57", "uuid": "61c83e2c-ffd2-4517-8353-c672a56d39e9"}, "group_in": {"src": "hda", "id": "842c471bdfd9c887", "uuid": "517541bb-1156-4c61-bda2-341c4bdbc22d"}, "alignreport_in": {"src": "hda", "id": "11a8d37cccceb071", "uuid": "137a99fb-0157-4241-9d36-1f71de3a69be"}, "list_in": {"src": "hda", "id": "c9e1a49c1225960d", "uuid": "cc505d11-a571-4e10-a752-a7f3a0e884b7"}, "name_in": {"src": "hda", "id": "70c3e648e0bbdb1c", "uuid": "353c65e1-e56a-4583-be0b-444eda6d964f"}}, "update_time": "2018-02-08T17:31:21.642906", "tool_id": "mothur_get_lineage", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "1be6bbaba2ffb15b", "uuid": "7ca3cacf-7b8c-4c88-b17e-422f35c7a299"}, "fasta_out": {"src": "hda", "id": "72a1145ce219300b", "uuid": "30f3f211-b8b0-4603-b9c8-c33ed578429b"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "cc260ebfc536bb4b", "uuid": "987a49be-eefe-4d4f-9ae4-f72c618fbfb0"}, "name_out": {"src": "hda", "id": "ab97b488b33c6246", "uuid": "35a651dd-bed5-4a1a-b77d-b8b25f7d88e2"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "efc416652e1b4600", "uuid": "4ed1729d-b356-48bf-b60c-e0fb10ee177f"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "b6539af83432ffdf", "uuid": "e4dd59a4-8400-4c8b-8179-b00ccc99bf8f"}, "__new_primary_file_unique|0.16__": {"src": "hda", "id": "31b6d67921f34be7", "uuid": "8e72d679-cfd8-47d7-b98c-9f6f22111f49"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "702034d3254f766a", "uuid": "e4f68036-9f09-44a8-a763-e05a6de05098"}, "__new_primary_file_unique|0.25__": {"src": "hda", "id": "41e9dee505e6f6ca", "uuid": "bd89b938-82d9-4993-8161-276f5a35b59f"}, "__new_primary_file_unique|0.15__": {"src": "hda", "id": "0da792b27e4b2b89", "uuid": "5185beb7-c38e-4ed2-bec0-9f2c91a67128"}, "__new_primary_file_unique|0.08__": {"src": "hda", "id": "b5decc7b8262a098", "uuid": "532f331d-6944-4dd5-8a1c-b7441f6b8a5e"}, "__new_primary_file_unique|0.14__": {"src": "hda", "id": "77b694bc117eb278", "uuid": "e12a1084-8f13-48ef-a3f6-146edd55811b"}, "__new_primary_file_unique|0.13__": {"src": "hda", "id": "c8578f7fa756d7dc", "uuid": "e4eb002f-a4a4-4544-bfa4-9870a934f008"}, "__new_primary_file_unique|0.09__": {"src": "hda", "id": "bc78784f4198424f", "uuid": "a08cc5b6-7e2d-444b-888d-112d58a2c302"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "ae6b27a2a1be3099", "uuid": "22bcbc31-0869-4336-a32f-e4d58103e730"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "c591040bd2b14dd3", "uuid": "9b1f67ef-057b-4613-acda-f0c5b8826759"}, "alignreport_out": {"src": "hda", "id": "1baefa50ed047fb0", "uuid": "c5b12544-fd55-41ad-a788-9decdb0f1bc3"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "543831fe8c81ade5", "uuid": "99208dbe-5ec3-4374-aaba-187815d1be6d"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "52c9abe36b090e71", "uuid": "4369cad3-3550-439d-a8f0-5c8c1ed28e2e"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "da3475a4d107f9d1", "uuid": "f25ff534-3003-4df5-8146-84e5167635e3"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "144a078b556f47ea", "uuid": "cdf8dcfc-f819-4c9c-9510-db1f9f05c3ce"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "652c409017f14add", "uuid": "ba8ee72c-2392-447e-86ad-75b27988c828"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "35abc15c823ac5f4", "uuid": "99be985a-c7ad-4f2f-af1d-948fec3666c1"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "8b2fddb4124acac3", "uuid": "17886915-baae-41ea-850b-63d48eeb1c95"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "3903fb6e0491d27a", "uuid": "92928c00-4d65-4244-b86f-4cf7c8dc3ea5"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "989b9f0457b89a0c", "uuid": "642287d6-7e73-4ac7-8fb3-bfc6d0d636b2"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "cd0b3415a2fdc60c", "uuid": "eac00c64-d9ee-4f7b-90ef-d55bb9b140e5"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "6c012b61d3ae01f5", "uuid": "c40d0e64-8dc4-4bb1-94d0-fdb98aa6a657"}, "logfile": {"src": "hda", "id": "d10cbc331e025114", "uuid": "25c3c7f7-2000-4396-b489-361f38da2e2d"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "8d8458d090ea7578", "uuid": "b8e4e7fa-032d-4fe8-99d0-60987b3bf8ff"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "a6ac437f8fe6da83", "uuid": "c961a1d0-d8aa-4859-96ec-a4b13b0e32a6"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "33b542efcfdd85ba", "uuid": "17c7677a-e8e1-468e-9124-3a8b486fa25f"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "6e25a68c2db30b46", "uuid": "fd6d2289-e2cd-4ee3-b979-0716f49fe7e4"}, "group_out": {"src": "hda", "id": "1baa7dc76fe18c68", "uuid": "f259dc8e-36fe-4e85-a55d-bf1992a8017d"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "2120d409550c595f", "uuid": "bed45e08-c284-49fa-9ce4-e418765ad6c8"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "4c9169af38dd62d7", "uuid": "bd68e773-91e9-4185-8ee9-81f4a853f391"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "bb3f644dc2fb6063", "uuid": "63a818fa-628d-42cb-8c21-69a8a9080aa1"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "38a761b89b9e6074", "uuid": "48f52554-6068-45cb-ab25-9a670e34afb6"}, "taxonomy_out": {"src": "hda", "id": "ed2ad3b822e9d9d3", "uuid": "6cf6e55c-2d40-4ae6-a182-299667b2a8cb"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "02434fd7d2885f87", "uuid": "a0205d2e-87a9-4052-8ce6-47d54c76632c"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "292bd36a691be581", "uuid": "c93c2459-e6a4-4d0e-9854-0756ffa9c70b"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "9552c7f8dd8e973e", "uuid": "3e07b209-bb24-4fff-8c0d-6db82c2c3664"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.lineage(taxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;-Bact \reria;Actinobacteria;',fasta=fasta_in.dat,group=group_in.dat,alignreport=alignrep \rort_in.dat,list=list_in.dat,name=name_in.dat,dups=true)\n[WARNING]: You did not provide a label, I will use the first label in your inputfile.\nYour file contains does not contain any sequences from Bacteria;Firmicutes;-Bacteria;Actinobacteria;.\nYour file contains does not contain any sequences from Bacteria;Firmicutes;-Bacteria;Actinobacteria;.\n\nOutput File Names: \nfile.taxonomy.pick.dat\nname_in.pick.dat\nfasta_in.pick.dat\ngroup_in.pick.dat\nalignreport_in.pick.align.report\nlist_in.unique.pick.dat\nlist_in.0.01.pick.dat\nlist_in.0.02.pick.dat\nlist_in.0.03.pick.dat\nlist_in.0.04.pick.dat\nlist_in.0.05.pick.dat\nlist_in.0.06.pick.dat\nlist_in.0.07.pick.dat\nlist_in.0.08.pick.dat\nlist_in.0.09.pick.dat\nlist_in.0.10.pick.dat\nlist_in.0.11.pick.dat\nlist_in.0.12.pick.dat\nlist_in.0.13.pick.dat\nlist_in.0.14.pick.dat\nlist_in.0.15.pick.dat\nlist_in.0.16.pick.dat\nlist_in.0.17.pick.dat\nlist_in.0.18.pick.dat\nlist_in.0.19.pick.dat\nlist_in.0.20.pick.dat\nlist_in.0.21.pick.dat\nlist_in.0.22.pick.dat\nlist_in.0.23.pick.dat\nlist_in.0.24.pick.dat\nlist_in.0.25.pick.dat\nlist_in.0.26.pick.dat\nlist_in.0.27.pick.dat\nlist_in.0.29.pick.dat\nlist_in.0.32.pick.dat\nlist_in.0.33.pick.dat\nlist_in.0.36.pick.dat\nlist_in.0.38.pick.dat\nlist_in.0.41.pick.dat\nlist_in.0.45.pick.dat\nlist_in.0.55.pick.dat\n\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1000.dat' file.taxonomy.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1001.dat' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1002.dat' group_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1003.dat' alignreport_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1004.dat' list_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1005.dat' name_in.dat && ln -s 'None' count.dat &&  echo 'get.lineage( taxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;-Bacteria;Actinobacteria;'\"' ,fasta=fasta_in.dat ,group=group_in.dat ,alignreport=alignreport_in.dat ,list=list_in.dat ,name=name_in.dat ,dups=true )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:31:14.507752", "params": {"count": "null", "dups": "\"true\"", "taxon": "\"Bacteria;Firmicutes;,Bacteria;Actinobacteria;\"", "dbkey": "\"hg17\"", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 1000}]}, \"filetype\": \"usetaxonomy\", \"taxons\": null, \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18531", "id": "349f287fcb778b99", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_lineage.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"file|taxonomy": {"src": "hda", "id": "6f78f21b003042c4"}, "file|taxons": ["Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Dorea(99);", "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(47);"], "file|filetype": "usetaxonomy"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "6f78f21b003042c4", "uuid": "a34f0692-a2db-4929-8627-e2e626069020"}}, "update_time": "2018-02-08T17:32:00.703931", "tool_id": "mothur_get_lineage", "outputs": {"logfile": {"src": "hda", "id": "fc9d58b578cf8af3", "uuid": "2490501b-95be-4366-b70a-7ac863f83736"}, "taxonomy_out": {"src": "hda", "id": "bdb1e7b62cbbd487", "uuid": "7afddbee-f1ec-4f8a-934d-2dcf0c5ed1ea"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.lineage(taxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;Clost \rridia;Clostridiales;Lachnospiraceae;Dorea;-Bacteria;Firmicutes;Clostridia;Clostr \ridiales;Lachnospiraceae;Roseburia;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1048.dat' file.taxonomy.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat &&  echo 'get.lineage( taxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Dorea;-Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Roseburia;'\"' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:31:57.562198", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 1048}]}, \"filetype\": \"usetaxonomy\", \"taxons\": [\"Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Dorea(99);\", \"Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(47);\"], \"__current_case__\": 0}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18638", "id": "f66e4e467d639b46", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_lineage.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"file|taxonomy": {"src": "hda", "id": "3747b718aaba1b94"}, "file|filetype": "useconstaxonomy", "taxon": "Bacteria;Bacteroidetes;"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "3747b718aaba1b94", "uuid": "848176ca-3663-40b3-ad42-2ca5bf3a3aa6"}}, "update_time": "2018-02-08T17:32:07.933961", "tool_id": "mothur_get_lineage", "outputs": {"logfile": {"src": "hda", "id": "40866b2ef26dac92", "uuid": "f1d9cb2c-7f1f-4fa5-91a9-d1a7f8bf7b48"}, "taxonomy_out": {"src": "hda", "id": "ad30ab610baf0fe8", "uuid": "90c595ff-def3-4094-80f8-7aeeadd6a528"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.lineage(constaxonomy=file.taxonomy.dat,taxon='Bacteria;Bacteroidete \rs;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1051.dat' file.taxonomy.dat && ln -s 'None' file.shared.dat && ln -s 'None' file.list.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat &&  echo 'get.lineage( constaxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Bacteroidetes;'\"' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:32:04.835077", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"Bacteria;Bacteroidetes;\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 1051}]}, \"filetype\": \"useconstaxonomy\", \"list\": null, \"taxons\": null, \"__current_case__\": 1, \"shared\": null}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18729", "id": "513510c2b856e80e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_lineage.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"file|taxonomy": {"src": "hda", "id": "1801e6a1fcd5e06c"}, "file|taxons": ["Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;", "Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;"], "file|filetype": "useconstaxonomy"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "1801e6a1fcd5e06c", "uuid": "e852ff59-b576-44ec-8a29-eac7fa18e1ba"}}, "update_time": "2018-02-08T17:32:15.209631", "tool_id": "mothur_get_lineage", "outputs": {"logfile": {"src": "hda", "id": "97f0f46b65c7979f", "uuid": "2ce2929d-499b-480c-8d75-1cf4bacf3de4"}, "taxonomy_out": {"src": "hda", "id": "9a6bce08b3fe7407", "uuid": "38612f05-7677-4b22-bafc-9ecaa5766156"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.lineage(constaxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;C \rlostridia;Clostridiales;Lachnospiraceae;unclassified;-Bacteria;Proteobacteria;Ga \rmmaproteobacteria;unclassified;unclassified;unclassified;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1054.dat' file.taxonomy.dat && ln -s 'None' file.shared.dat && ln -s 'None' file.list.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat &&  echo 'get.lineage( constaxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;unclassified;-Bacteria;Proteobacteria;Gammaproteobacteria;unclassified;unclassified;unclassified;'\"' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:32:12.085958", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 1054}]}, \"filetype\": \"useconstaxonomy\", \"list\": null, \"taxons\": [\"Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;\", \"Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;\"], \"__current_case__\": 1, \"shared\": null}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18823", "id": "25de304670fe7732", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_lineage.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"input|filetype": "group", "input|infile": {"src": "hda", "id": "89d9aa21c72ed3c7"}}, "job": {"inputs": {"infile": {"src": "hda", "id": "89d9aa21c72ed3c7", "uuid": "488e2f2d-d7ae-452d-898f-9f6f1d80ea64"}}, "update_time": "2018-02-08T17:32:22.411197", "tool_id": "mothur_get_mimarkspackage", "outputs": {"logfile": {"src": "hda", "id": "8013a1d7cf129351", "uuid": "c2d1a36f-3d5b-48c8-a2e5-ed63db8e4ec0"}, "package_out": {"src": "hda", "id": "426b952bd444adde", "uuid": "354ae98b-75db-4e76-9d1f-e7318f16b114"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.mimarkspackage(group=input.infile.dat,package=miscellaneous,require \rdonly=false)\n\nOutput File Names: \ninput.infile.tsv\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1057.dat' input.infile.dat &&  echo 'get.mimarkspackage( group=input.infile.dat, package=miscellaneous, requiredonly=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:32:19.295899", "params": {"input": "{\"filetype\": \"group\", \"infile\": {\"values\": [{\"src\": \"hda\", \"id\": 1057}]}, \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "requiredonly": "\"false\"", "dbkey": "\"hg17\"", "package": "\"miscellaneous\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "18920", "id": "d57022ef22692475", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_mimarkspackage.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"package": "human_associated", "input|filetype": "oligos", "requiredonly": true, "input|infile": {"src": "hda", "id": "4a96cd4627e246f4"}}, "job": {"inputs": {"infile": {"src": "hda", "id": "4a96cd4627e246f4", "uuid": "388018a5-3429-42ff-a1c6-82941ad8176c"}}, "update_time": "2018-02-08T17:32:39.918619", "tool_id": "mothur_get_mimarkspackage", "outputs": {"logfile": {"src": "hda", "id": "3190333ac07edb13", "uuid": "227555a5-3417-4443-a05f-1a8f6b461e65"}, "package_out": {"src": "hda", "id": "234cb682c356f1ab", "uuid": "1e5c3119-a427-4614-a687-49a89283a86a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.mimarkspackage(oligos=input.infile.dat,package=human_associated,req \ruiredonly=true)\n\nOutput File Names: \ninput.infile.tsv\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1060.dat' input.infile.dat &&  echo 'get.mimarkspackage( oligos=input.infile.dat, package=human_associated, requiredonly=true )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:32:36.779382", "params": {"input": "{\"filetype\": \"oligos\", \"infile\": {\"values\": [{\"src\": \"hda\", \"id\": 1060}]}, \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "requiredonly": "\"true\"", "dbkey": "\"hg17\"", "package": "\"human_associated\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19016", "id": "9b36a3aa47b79bf2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_mimarkspackage.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"infile|label": "0.22", "accnos": {"src": "hda", "id": "7655e53fa1ea970d"}, "infile|otu": {"src": "hda", "id": "df211d5332576ec7"}, "infile|intype": "in_shared"}, "job": {"inputs": {"accnos": {"src": "hda", "id": "7655e53fa1ea970d", "uuid": "a4d2e512-5b1e-40a8-9426-0dd4f92d86ea"}, "otu": {"src": "hda", "id": "df211d5332576ec7", "uuid": "2039f857-077f-4c50-9567-19e37479e17b"}}, "update_time": "2018-02-08T17:33:00.529600", "tool_id": "mothur_get_otulabels", "outputs": {"pick_out": {"src": "hda", "id": "75d344c42dc42fbd", "uuid": "280149a7-f5ed-42f7-8baf-92b5769c1742"}, "logfile": {"src": "hda", "id": "dca46da602361c10", "uuid": "5f8de98c-4fd6-495a-820f-be954f81dd62"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.otulabels(shared=infile.otu.dat,label=0.22,accnos=accnos.dat)\nYour file does not contain any OTUs from the .accnos file.\nSelected 0 OTUs from your shared file.\n\nOutput File Names: \ninfile.otu.0.22.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1064.dat' infile.otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1063.dat' accnos.dat &&  echo 'get.otulabels( shared=infile.otu.dat, label=0.22, accnos=accnos.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:32:57.371646", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1064}]}, \"__current_case__\": 0, \"label\": \"0.22\"}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19126", "id": "24a1da3a8e5693fe", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_otulabels.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"infile|intype": "in_other", "accnos": {"src": "hda", "id": "34e6c2e9e95d8f5b"}, "infile|otu": {"src": "hda", "id": "99e402de1bba2f0d"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "34e6c2e9e95d8f5b", "uuid": "4929e9c0-5b6b-4f48-a881-487a21d2202c"}, "otu": {"src": "hda", "id": "99e402de1bba2f0d", "uuid": "d40ef2c8-d38f-435a-b210-2b21774b9155"}}, "update_time": "2018-02-08T17:33:21.098179", "tool_id": "mothur_get_otulabels", "outputs": {"pick_out": {"src": "hda", "id": "22857389d798733d", "uuid": "8a727fb8-62de-4743-933f-6046086727fa"}, "logfile": {"src": "hda", "id": "f079ce0ad2349821", "uuid": "fffb75ac-8124-4205-9fff-c61e61e3471b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.otulabels(corraxes=infile.otu.dat,accnos=accnos.dat)\nSelected 3 lines from your corr.axes file.\n\nOutput File Names: \ninfile.otu.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1068.dat' infile.otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1067.dat' accnos.dat &&  echo 'get.otulabels( corraxes=infile.otu.dat, accnos=accnos.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:33:17.955974", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_other\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1068}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19238", "id": "8543024575f6f30b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_otulabels.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "51b6da2201439bf7"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "51b6da2201439bf7", "uuid": "51f6010d-d1d0-46d1-89ee-3bfbcab06111"}}, "update_time": "2018-02-08T17:33:40.377632", "tool_id": "mothur_get_otulist", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "c778881db4f7e02e", "uuid": "b173a65d-467c-4045-bee3-fbdf52304014"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "eb9c10339397af09", "uuid": "be8ed080-334f-4c29-ae4e-367049fb2a97"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "f9a0977992bfb9ba", "uuid": "2d0a77a9-0751-4610-bc66-25ab889081d0"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "e6a4ded894b6f5fa", "uuid": "8beb9edc-760a-42da-af4c-953585c0ca25"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "3bf74cdfe204f463", "uuid": "5ab3735f-5d97-493d-b0ff-4ce508562fea"}, "__new_primary_file_unique|0.16__": {"src": "hda", "id": "153ecf05259735e5", "uuid": "773eef8c-a03e-438f-aac0-b954b1b32ab6"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "4ba65871d102d69d", "uuid": "3c40c6ca-758d-4b93-8821-e375a1267e0d"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "1e62b3b8018b2fc6", "uuid": "600dfbaa-4811-47a3-84e3-dc7c90c84a0d"}, "__new_primary_file_unique|0.15__": {"src": "hda", "id": "8fe9921e6d7dbafc", "uuid": "a5392bd0-046a-4266-a9a0-152c9e451f92"}, "__new_primary_file_unique|0.08__": {"src": "hda", "id": "68a07b8eb9e4a63b", "uuid": "aee16746-2c8e-4fc6-990a-c5cee5436cdb"}, "__new_primary_file_unique|0.14__": {"src": "hda", "id": "f2786a3b53d84563", "uuid": "a5ad18f2-5b98-45f6-802c-dc87a6d11c4a"}, "__new_primary_file_unique|0.13__": {"src": "hda", "id": "2ddd0affa57a5a37", "uuid": "df7243a2-ecce-4d2e-a4be-430ad666cf9f"}, "__new_primary_file_unique|0.09__": {"src": "hda", "id": "cb6f70c43fa71834", "uuid": "2947c836-d283-484c-a40e-cd893227cc87"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "68f8799b51cd39a2", "uuid": "7ed1c56c-a6b8-4516-a523-7026512de1df"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "62147ed004c8781f", "uuid": "4e8c99c2-5413-4073-abd2-0e3af081b082"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "6666372c4fab48c4", "uuid": "9af8f2b5-b3db-4d45-b716-920429a85b0f"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "eb38b861ea77d447", "uuid": "eea105e0-ad99-4952-a69a-d5a6761d334d"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "9f7279a088a67da9", "uuid": "18e2c6cf-65e7-49cd-99f3-08efa94556ce"}, "__new_primary_file_unique|0.25__": {"src": "hda", "id": "9a4581073136ed09", "uuid": "6f6ce176-5ef2-4e40-bb91-77e7f9dedc47"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "f38022c92a0f7f7b", "uuid": "4cf0fa53-3f7e-45a6-ab9d-806e15f7903c"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "708b991ac9f806e1", "uuid": "17f747ef-57f5-49ad-aee7-458525b4ce6f"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "5bc01bd5935f41c1", "uuid": "683c7d93-6656-4a64-932a-f6034f55246a"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "2d25c0be08883c54", "uuid": "0ff99942-64cc-40cb-b1ad-96c25c2028aa"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "4a58f5a4317a3c0d", "uuid": "dda6a4e9-ded3-403e-8e94-9fc84e6acba7"}, "logfile": {"src": "hda", "id": "5b67fe605870f3c1", "uuid": "0ce5e213-7fb1-4789-8ded-a50cf998d596"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "b2e7f29c6e6f4615", "uuid": "68ac73b3-6188-4a84-9f67-803eeb8a4820"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "84bd3054481cbbc7", "uuid": "ff4452b9-605a-4c94-985e-81af102ec3db"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "ab352c0b18312637", "uuid": "531c68fc-392f-4651-9657-06386d0015c1"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "e47a18097101ae28", "uuid": "126ff3b8-6f66-4bd6-9c7e-d8df71e54451"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "e9997d6b1fbf571c", "uuid": "c43a5aec-e58e-4ba6-8157-12407ee64a4a"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "c1b250e6ee924774", "uuid": "d5ba1691-b71e-46e9-8035-cdbf7853d7e5"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "ac2a2c496e4cb460", "uuid": "67de3c2d-4d07-4d49-a71f-33e9dec1d5dd"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "ba8455fb60b4981e", "uuid": "c2308bf6-aa53-4d11-94a0-ce788ada056e"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "6c06a1831dcb5d3f", "uuid": "2eb4ca1e-3619-410f-b26e-e2f1a5f05b6e"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "89a5a72f6f25aac7", "uuid": "a1d0db62-1e7d-467f-96e0-c78875629ddd"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "71ce468762f23cf3", "uuid": "97a17ca3-ec2c-4024-8c88-04505a334415"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "6b320855e1131164", "uuid": "b47f9106-ecc3-4128-8d22-bb8ca5e63fe1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.otulist(list=otu.dat,sort=otu)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.otu\notu.0.01.otu\notu.0.02.otu\notu.0.03.otu\notu.0.04.otu\notu.0.05.otu\notu.0.06.otu\notu.0.07.otu\notu.0.08.otu\notu.0.09.otu\notu.0.10.otu\notu.0.11.otu\notu.0.12.otu\notu.0.13.otu\notu.0.14.otu\notu.0.15.otu\notu.0.16.otu\notu.0.17.otu\notu.0.18.otu\notu.0.19.otu\notu.0.20.otu\notu.0.21.otu\notu.0.22.otu\notu.0.23.otu\notu.0.24.otu\notu.0.25.otu\notu.0.26.otu\notu.0.27.otu\notu.0.29.otu\notu.0.32.otu\notu.0.33.otu\notu.0.36.otu\notu.0.38.otu\notu.0.41.otu\notu.0.45.otu\notu.0.55.otu\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1071.dat' otu.dat &&  echo 'get.otulist( list=otu.dat, sort=otu )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:33:35.450862", "params": {"sort": "\"otu\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19324", "id": "c8288be11b30d2bc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_otulist.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "a2c166d4f307d0c8"}, "label": ["0.03", "0.38", "0.41", "0.45"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "a2c166d4f307d0c8", "uuid": "d782722b-b6ac-4f74-9bbc-c412dec690a0"}}, "update_time": "2018-02-08T17:33:59.277768", "tool_id": "mothur_get_otulist", "outputs": {"__new_primary_file_0.45|0.03__": {"src": "hda", "id": "3d2f7571dd3f526d", "uuid": "3a4dbde5-5d8f-4749-bae9-8cc89431844e"}, "logfile": {"src": "hda", "id": "d6e970b870fc412a", "uuid": "b4bea723-db34-4add-82fa-88018028a987"}, "__new_primary_file_0.45|0.41__": {"src": "hda", "id": "07562b49fba381a7", "uuid": "bb6b1e54-2bcd-4c2b-9524-1b7b9116beaf"}, "__new_primary_file_0.45|0.38__": {"src": "hda", "id": "ba7c7bcdabc0857e", "uuid": "7adf7cf1-dcd0-47fc-9848-c7882490fb65"}, "__new_primary_file_0.45|0.45__": {"src": "hda", "id": "d2fb07980323f68c", "uuid": "6f62cad4-b96a-481b-a5a4-b8665aeb88dc"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.otulist(list=otu.dat,label=0.03-0.38-0.41-0.45,sort=otu)\n0.03\n0.38\n0.41\n0.45\n\nOutput File Names: \notu.0.03.otu\notu.0.38.otu\notu.0.41.otu\notu.0.45.otu\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1109.dat' otu.dat &&  echo 'get.otulist( list=otu.dat, label=0.03-0.38-0.41-0.45, sort=otu )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:33:56.020360", "params": {"sort": "\"otu\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.38\", \"0.41\", \"0.45\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19410", "id": "466b5293998bb5d6", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_otulist.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"method_condition|matrix_condition|dist": {"src": "hda", "id": "416075c69c435f24"}, "method_condition|method_switch": "distance", "method_condition|matrix_condition|matrix_format": "phylip", "method_condition|matrix_condition|nameOrCount": {"src": "hda", "id": "41fd880cfa9a87dd"}, "otu": {"src": "hda", "id": "93a3cb8d32c9fc8d"}}, "job": {"inputs": {"method_condition|dist": {"src": "hda", "id": "416075c69c435f24", "uuid": "651b1fe5-7d73-42e9-abc3-337dc0082bc4"}, "otu": {"src": "hda", "id": "93a3cb8d32c9fc8d", "uuid": "e3460105-26cd-46af-8ab3-19b8cc079558"}, "method_condition|nameOrCount": {"src": "hda", "id": "41fd880cfa9a87dd", "uuid": "7369cd69-029a-46dd-b78d-c926c82835b4"}}, "update_time": "2018-02-08T17:34:25.314721", "tool_id": "mothur_get_oturep", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "30bdbac696e3ceef", "uuid": "d00fedc6-1efb-42e4-b37f-f45f957e2b92"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "da8aa8fdc0218a93", "uuid": "8361ade7-0f32-46f2-a1a8-8ee6da9ce758"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "730ca47799cf02d3", "uuid": "c4c5a461-029b-4cc1-a593-68c5ce286fde"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "40c1ea605096e77f", "uuid": "904130ae-a436-4559-8ffc-a6b7c5afe75b"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "2f333f7cf7d78907", "uuid": 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"uuid": "229d4590-77d5-4fed-89d2-09075640edde"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "0f0ea7742d2f7a9c", "uuid": "4c270c1a-b961-4106-afd3-5561dffb11c8"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "5b683d70bee32138", "uuid": "43437a44-842b-463d-abd6-0a5d964ea42c"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "24f92017f4321b90", "uuid": "9fcc26f4-d414-4037-acd8-5f5740d46cba"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "f9659e23aabc1e0c", "uuid": "8830819f-b9d2-4e58-9ca9-577c70136f8c"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "e1bf44ffb4951bed", "uuid": "32267982-3d31-4cd7-ae5d-9864dbff86c8"}, "__new_primary_file_unique|0.25__": {"src": "hda", "id": "44b7656f117551f6", "uuid": "eb7395a0-011b-4a13-bafb-eeab65b98b20"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "51c23b5ceed9c18d", "uuid": "d172a29d-bb33-4b2c-a2f6-d91bde3b546f"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "1048228746240cdf", "uuid": "8459e654-0094-4c4e-87ce-9f5b73061296"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "723e4e10e4eecc59", "uuid": "029e3382-9a04-4548-baa2-e63b84d11e16"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "db87f06412e7adc0", "uuid": "c238c158-81e4-400b-85cf-28fcd2dd4061"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "00e13cdc183f52a5", "uuid": "cba7bc5b-73b3-4620-9218-7533386b618f"}, "logfile": {"src": "hda", "id": "f78a9bc7e1b3c5b0", "uuid": "a882b0e9-9a6f-4d01-915f-911d89ce8a26"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "8fc6a110eb2265d3", "uuid": "acbd8207-5ea5-40c0-9cd1-a60c84ddedfb"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "d4eed87b276e13c1", "uuid": "c9dadca8-883f-4f02-8bb8-bdc3908015c2"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "d19ff3dd0342839a", "uuid": "b18b0941-7b73-4b1f-a8db-5460a0cd2c57"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "19a46808e9dc1c5e", "uuid": "751d8de8-ddf8-40ed-863d-ba0e09096f8b"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "fe4f1a00cf04fcf3", "uuid": "1fca2b37-632d-40ba-b337-31b86a484895"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "555713c20c62ccd8", "uuid": "611a22bc-02f3-43ba-af20-d309b5e3f6db"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "7d80d946c53c84eb", "uuid": "7d937db3-7669-48c8-ac91-7c6f22dd7604"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "1fe9146927bcc3d0", "uuid": "cf5a33eb-e7c1-4396-a03b-c17a9ad4c3d0"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "7da19e3d7c19664a", "uuid": "35d9c97d-f75c-4881-bb73-cf9c906638f5"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "9c891a5a995773c1", "uuid": "485aaddf-1d54-47a0-baf6-85f127aff543"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "8281173e1dd8fbe2", "uuid": "5ed26988-c989-4ca7-a830-54782b46355b"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "f2d7713593c3c9fc", "uuid": "86ef6768-6f66-4e03-a4ce-127adc736dcd"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.oturep(list=otu.dat,method=distance,phylip=dist.dat,name=nameOrCoun \rt.dat,large=false)\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\nunique\t96\n0.01\t93\n0.02\t90\n0.03\t88\n0.04\t83\n0.05\t78\n0.06\t69\n0.07\t65\n0.08\t56\n0.09\t55\n0.10\t49\n0.11\t45\n0.12\t43\n0.13\t40\n0.14\t36\n0.15\t35\n0.16\t34\n0.17\t33\n0.18\t31\n0.19\t30\n0.20\t27\n0.21\t25\n0.22\t23\n0.23\t21\n0.24\t17\n0.25\t15\n0.26\t13\n0.27\t12\n0.29\t9\n0.32\t7\n0.33\t6\n0.36\t5\n0.38\t4\n0.41\t3\n0.45\t2\n0.55\t1\n\nOutput File Names: \notu.unique.rep.names\notu.0.01.rep.names\notu.0.02.rep.names\notu.0.03.rep.names\notu.0.04.rep.names\notu.0.05.rep.names\notu.0.06.rep.names\notu.0.07.rep.names\notu.0.08.rep.names\notu.0.09.rep.names\notu.0.10.rep.names\notu.0.11.rep.names\notu.0.12.rep.names\notu.0.13.rep.names\notu.0.14.rep.names\notu.0.15.rep.names\notu.0.16.rep.names\notu.0.17.rep.names\notu.0.18.rep.names\notu.0.19.rep.names\notu.0.20.rep.names\notu.0.21.rep.names\notu.0.22.rep.names\notu.0.23.rep.names\notu.0.24.rep.names\notu.0.25.rep.names\notu.0.26.rep.names\notu.0.27.rep.names\notu.0.29.rep.names\notu.0.32.rep.names\notu.0.33.rep.names\notu.0.36.rep.names\notu.0.38.rep.names\notu.0.41.rep.names\notu.0.45.rep.names\notu.0.55.rep.names\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1115.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1116.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1117.dat' nameOrCount.dat && ln -s 'None' fasta.dat &&  echo 'get.oturep( list=otu.dat, method=distance, phylip=dist.dat, name=nameOrCount.dat, large=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:34:19.832670", "params": {"sorted": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method_condition": "{\"matrix_condition\": {\"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 1117}]}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 1116}]}, \"__current_case__\": 1, \"matrix_format\": \"phylip\"}, \"large\": \"false\", \"__current_case__\": 0, \"pick\": {\"type\": \"no\", \"__current_case__\": 0}, \"fasta\": null, \"method_switch\": \"distance\"}", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19539", "id": "8078f99fccaa607a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_oturep.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"method_condition|matrix_condition|dist": {"src": "hda", "id": "aed4888e53be2c29"}, "method_condition|method_switch": "distance", "label": ["unique", "0.05", "0.27", "0.45"], "method_condition|matrix_condition|matrix_format": "column", "method_condition|matrix_condition|nameOrCount": {"src": "hda", "id": "73d20dc7f05cb923"}, "otu": {"src": "hda", "id": "0fb95b6100ab75ac"}}, "job": {"inputs": {"method_condition|dist": {"src": "hda", "id": "aed4888e53be2c29", "uuid": "96cd93f8-13f1-4f66-91f7-f472d543e547"}, "otu": {"src": "hda", "id": "0fb95b6100ab75ac", "uuid": "5ffb4a90-dbe5-4368-9174-0b8e26c34032"}, "method_condition|nameOrCount": {"src": "hda", "id": "73d20dc7f05cb923", "uuid": "c6cb40a8-1e8d-44bf-a814-70d1f319f2b8"}}, "update_time": "2018-02-08T17:34:50.940943", "tool_id": "mothur_get_oturep", "outputs": {"__new_primary_file_unique|0.27__": {"src": "hda", "id": "ca68502e42c4e7cc", "uuid": "912df286-c4c3-4ada-b486-05d0ffb119df"}, "logfile": {"src": "hda", "id": "d1da4bfb123cb5f7", "uuid": "96a5082d-9fc0-4b22-9a61-66513477c1d4"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "b385cc8f12ae4655", "uuid": "f10d0810-0145-4cba-8dbc-39c44f07d928"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "f5a2e6053244a622", "uuid": "e46476d5-e0a7-486f-a012-e2f903c615b5"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "13c1cf6c966b3c28", "uuid": "39f76377-6d8a-4358-94e0-b5e54fd992cb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.oturep(list=otu.dat,label=unique-0.05-0.27-0.45,method=distance,col \rumn=dist.dat,name=nameOrCount.dat,large=false)\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\nunique\t96\n0.05\t78\n0.27\t12\n0.45\t2\n\nOutput File Names: \notu.unique.rep.names\notu.0.05.rep.names\notu.0.27.rep.names\notu.0.45.rep.names\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1155.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1156.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1157.dat' nameOrCount.dat && ln -s 'None' fasta.dat &&  echo 'get.oturep( list=otu.dat, label=unique-0.05-0.27-0.45, method=distance, column=dist.dat, name=nameOrCount.dat, large=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:34:47.568188", "params": {"sorted": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method_condition": "{\"matrix_condition\": {\"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 1157}]}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 1156}]}, \"__current_case__\": 0, \"matrix_format\": \"column\"}, \"large\": \"false\", \"__current_case__\": 0, \"pick\": {\"type\": \"no\", \"__current_case__\": 0}, \"fasta\": null, \"method_switch\": \"distance\"}", "dbkey": "\"hg17\"", "label": "[\"unique\", \"0.05\", \"0.27\", \"0.45\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19677", "id": "aa70baf734620bdc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_oturep.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"method_condition|matrix_condition|dist": {"src": "hda", "id": "b7f71ad5197d9e0a"}, "method_condition|method_switch": "distance", "label": ["0.05", "0.27"], "method_condition|fasta": {"src": "hda", "id": "dec68a77ca6fab55"}, "sorted": "name", "method_condition|matrix_condition|matrix_format": "phylip", "otu": {"src": "hda", "id": "8bcaa6ddefe62301"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "dec68a77ca6fab55", "uuid": "920ebc87-4daf-49bb-91ba-0cf172a8a7dc"}, "method_condition|dist": {"src": "hda", "id": "b7f71ad5197d9e0a", "uuid": "92fe70a5-1c0a-49a6-935a-b931d3a5ec9f"}, "otu": {"src": "hda", "id": "8bcaa6ddefe62301", "uuid": "da9a90c4-f59b-45f4-9450-e14e8ee4c35d"}}, "update_time": "2018-02-08T17:35:18.183092", "tool_id": "mothur_get_oturep", "outputs": {"logfile": {"src": "hda", "id": "a3c766aaa70cf6ac", "uuid": "efc1c573-1a6b-41d7-81a4-76689dcc7e00"}, "__new_primary_file_0.27|0.27__": {"src": "hda", "id": "e52776a59fe07134", "uuid": "5a7ca434-6a13-4855-8a02-e98754a14ca1"}, "__new_primary_file_0.27|0.05__": {"src": "hda", "id": "d4a90b8ec5d7a12a", "uuid": "07714f97-9622-4c39-a222-ec47f5cf059b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.oturep(list=otu.dat,sorted=name,label=0.05-0.27,method=distance,phy \rlip=dist.dat,fasta=fasta.dat,large=false)\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n0.05\t78\n0.27\t12\n\nOutput File Names: \notu.0.05.rep.names\notu.0.27.rep.names\notu.0.05.rep.fasta\notu.0.27.rep.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1163.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1164.dat' dist.dat && ln -s 'None' nameOrCount.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1165.dat' fasta.dat &&  echo 'get.oturep( list=otu.dat, sorted=name, label=0.05-0.27, method=distance, phylip=dist.dat, fasta=fasta.dat, large=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:35:14.684754", "params": {"sorted": "\"name\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method_condition": "{\"matrix_condition\": {\"nameOrCount\": null, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 1164}]}, \"__current_case__\": 1, \"matrix_format\": \"phylip\"}, \"large\": \"false\", \"__current_case__\": 0, \"pick\": {\"type\": \"no\", \"__current_case__\": 0}, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 1165}]}, \"method_switch\": \"distance\"}", "dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.27\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19808", "id": "3b972a2e0d2ad508", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_oturep.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"method_condition|matrix_condition|dist": {"src": "hda", "id": "bd8b611863ed9308"}, "method_condition|pick|type": "yes", "method_condition|method_switch": "distance", "method_condition|pick|groups": ["forest", "pasture"], "label": ["unique", "0.05", "0.27", "0.45"], "method_condition|pick|group": {"src": "hda", "id": "880bb69112fd68b6"}, "method_condition|matrix_condition|matrix_format": "column", "method_condition|matrix_condition|nameOrCount": {"src": "hda", "id": "d3518d8bb3652466"}, "otu": {"src": "hda", "id": "99ed50059af5bb02"}}, "job": {"inputs": {"method_condition|dist": {"src": "hda", "id": "bd8b611863ed9308", "uuid": "0cb40344-36cb-44fb-a8cc-d07691846f66"}, "method_condition|group": {"src": "hda", "id": "880bb69112fd68b6", "uuid": "b205373d-838d-4be6-9e37-3bfa2b3382d3"}, "method_condition|nameOrCount": {"src": "hda", "id": "d3518d8bb3652466", "uuid": "af6179b3-ab69-450c-8357-6407ea905dd6"}, "otu": {"src": "hda", "id": "99ed50059af5bb02", "uuid": "fe690c4f-e026-44af-b323-634907cdf208"}}, "update_time": "2018-02-08T17:35:53.329170", "tool_id": "mothur_get_oturep", "outputs": {"__new_primary_file_unique.pasture|0.45.pasture__": {"src": "hda", "id": "fd31441a4aa60ede", "uuid": "544892b7-e41c-48c3-8897-89fa5c24865e"}, "__new_primary_file_unique.pasture|0.05.forest__": {"src": "hda", "id": "777ec9c5caa78d86", "uuid": "5301c818-c0f1-4e1d-94c8-06a2fdd5667b"}, "__new_primary_file_unique.pasture|0.45.forest__": {"src": "hda", "id": "d6f1701a9167dd73", "uuid": "814d1e54-4320-46a1-a6dd-c3d0f0d2ddc3"}, "__new_primary_file_unique.pasture|0.27.forest__": {"src": "hda", "id": "9faf5e4358ec058f", "uuid": "3ddef2ce-68da-40ef-943a-4d7a1fa8627f"}, "__new_primary_file_unique.pasture|0.27.pasture__": {"src": "hda", "id": "7543a3403ae6979a", "uuid": "9f91fa26-e088-4c63-853d-5f9c14989542"}, "__new_primary_file_unique.pasture|unique.forest__": {"src": "hda", "id": "fde429e6e97b9f81", "uuid": "480db91e-8bbf-4a1d-85f1-890eb1ec7265"}, "__new_primary_file_unique.pasture|unique.pasture__": {"src": "hda", "id": "f408fc8f9300835d", "uuid": "10810240-3e47-4233-b28c-189c679d5571"}, "__new_primary_file_unique.pasture|0.05.pasture__": {"src": "hda", "id": "93aeb4de827d6c47", "uuid": "bd646759-619e-4204-94c1-0432fc92542c"}, "logfile": {"src": "hda", "id": "f87690ae06d59048", "uuid": "27b54f17-ddd9-4c42-a15b-894f8a8a5ea3"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.oturep(list=otu.dat,label=unique-0.05-0.27-0.45,method=distance,col \rumn=dist.dat,name=nameOrCount.dat,group=group.dat,groups=forest-pasture,large=fa \rlse)\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\nunique\t96\n0.05\t78\n0.27\t12\n0.45\t2\n\nOutput File Names: \notu.unique.forest.rep.names\notu.unique.pasture.rep.names\notu.0.05.forest.rep.names\notu.0.05.pasture.rep.names\notu.0.27.forest.rep.names\notu.0.27.pasture.rep.names\notu.0.45.forest.rep.names\notu.0.45.pasture.rep.names\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1171.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1172.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1173.dat' nameOrCount.dat && ln -s 'None' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1174.dat' group.dat &&  echo 'get.oturep( list=otu.dat, label=unique-0.05-0.27-0.45, method=distance, column=dist.dat, name=nameOrCount.dat, group=group.dat, groups=forest-pasture, large=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:35:49.660708", "params": {"sorted": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method_condition": "{\"matrix_condition\": {\"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 1173}]}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 1172}]}, \"__current_case__\": 0, \"matrix_format\": \"column\"}, \"large\": \"false\", \"__current_case__\": 0, \"pick\": {\"group\": {\"values\": [{\"src\": \"hda\", \"id\": 1174}]}, \"type\": \"yes\", \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 1}, \"fasta\": null, \"method_switch\": \"distance\"}", "dbkey": "\"hg17\"", "label": "[\"unique\", \"0.05\", \"0.27\", \"0.45\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "19976", "id": "ffc368cd972b6cba", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_oturep.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"method_condition|matrix_condition|dist": {"src": "hda", "id": "958f42f7df38196a"}, "method_condition|method_switch": "distance", "label": ["unique", "0.05", "0.27"], "method_condition|matrix_condition|matrix_format": "phylip", "method_condition|matrix_condition|nameOrCount": {"src": "hda", "id": "000295148157cfd1"}, "otu": {"src": "hda", "id": "373650fcf8f1288e"}}, "job": {"inputs": {"method_condition|dist": {"src": "hda", "id": "958f42f7df38196a", "uuid": "400e1660-0d20-4d5c-830a-3772755a3393"}, "otu": {"src": "hda", "id": "373650fcf8f1288e", "uuid": "07cf7628-7743-4274-a93e-de87a21c1ccf"}, "method_condition|nameOrCount": {"src": "hda", "id": "000295148157cfd1", "uuid": "fc4b5d83-a6f1-45de-b081-d489ab5d6fd3"}}, "update_time": "2018-02-08T17:36:19.731566", "tool_id": "mothur_get_oturep", "outputs": {"__new_primary_file_unique|0.27__": {"src": "hda", "id": "333420e1d962f11c", "uuid": "4df77d09-1a1f-408d-b20e-042b1034ec40"}, "logfile": {"src": "hda", "id": "df814c1a97206794", "uuid": "4f24dc30-58c5-4090-b123-c1d740dda48e"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "0eb134575c8781c5", "uuid": "4e4a889b-eac7-456a-b098-c81ec17a6690"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "0f8c488416e0bcc6", "uuid": "4e9b21fb-c2f3-4e3f-99a3-ef7edc44b7a3"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.oturep(list=otu.dat,label=unique-0.05-0.27,method=distance,phylip=d \rist.dat,count=nameOrCount.dat,large=false)\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\nunique\t96\n0.05\t78\n0.27\t12\n\nOutput File Names: \notu.unique.rep.count_table\notu.0.05.rep.count_table\notu.0.27.rep.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1184.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1185.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1186.dat' nameOrCount.dat && ln -s 'None' fasta.dat &&  echo 'get.oturep( list=otu.dat, label=unique-0.05-0.27, method=distance, phylip=dist.dat, count=nameOrCount.dat, large=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:36:16.372153", "params": {"sorted": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method_condition": "{\"matrix_condition\": {\"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 1186}]}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 1185}]}, \"__current_case__\": 1, \"matrix_format\": \"phylip\"}, \"large\": \"false\", \"__current_case__\": 0, \"pick\": {\"type\": \"no\", \"__current_case__\": 0}, \"fasta\": null, \"method_switch\": \"distance\"}", "dbkey": "\"hg17\"", "label": "[\"unique\", \"0.05\", \"0.27\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20116", "id": "555065f5aff402d2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_oturep.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"method_condition|method_switch": "abundance", "sorted": "name", "otu": {"src": "hda", "id": "d833ede7810d07eb"}, "method_condition|nameOrCount": {"src": "hda", "id": "d98e0261251f3c05"}, "label": ["0.27", "unique"]}, "job": {"inputs": {"nameOrCount": {"src": "hda", "id": "d98e0261251f3c05", "uuid": "8ec5ddb4-55fd-4945-9e26-1b1a27ce00ca"}, "otu": {"src": "hda", "id": "d833ede7810d07eb", "uuid": "78a8119d-6cfb-4966-b6a8-e8a9bfd6d4c5"}}, "update_time": "2018-02-08T17:36:43.502738", "tool_id": "mothur_get_oturep", "outputs": {"__new_primary_file_unique|0.27__": {"src": "hda", "id": "9323df72f1a4c803", "uuid": "8478ad40-7eff-4304-b99b-0f4f722801c5"}, "logfile": {"src": "hda", "id": "9e9b9c71a17f9730", "uuid": "8db390b1-489a-42db-90e1-b0f5c2534c60"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "5f798f9781df9c30", "uuid": "a377f0e3-2c9e-4de5-b1e9-cb6ef2872533"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.oturep(list=otu.dat,sorted=name,label=0.27-unique,method=abundance, \rcount=nameOrCount.dat)\nunique\t96\n0.27\t12\n\nOutput File Names: \notu.unique.rep.count_table\notu.0.27.rep.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1191.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1192.dat' nameOrCount.dat &&  echo 'get.oturep( list=otu.dat, sorted=name, label=0.27-unique, method=abundance, count=nameOrCount.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:36:40.304148", "params": {"sorted": "\"name\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method_condition": "{\"nameOrCount\": {\"values\": [{\"src\": \"hda\", \"id\": 1192}]}, \"method_switch\": \"abundance\", \"__current_case__\": 1}", "dbkey": "\"hg17\"", "label": "[\"0.27\", \"unique\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20233", "id": "ea74846895a98ad3", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_oturep.test_tool_000005", "has_data": true}, {"data": {"status": "success", "inputs": {"accnos": {"src": "hda", "id": "a1bc33c7c6bf579d"}, "list": {"src": "hda", "id": "a2471179f56050c1"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "a1bc33c7c6bf579d", "uuid": "68ae3019-f0dc-4923-824d-edfddc8d9060"}, "list": {"src": "hda", "id": "a2471179f56050c1", "uuid": "34e8f19e-acf8-4c08-a1b1-c9ef0e042628"}}, "update_time": "2018-02-08T17:37:04.284293", "tool_id": "mothur_get_otus", "outputs": {"corraxes_out": {"src": "hda", "id": "981110199526228d", "uuid": "9cefca4b-082e-4454-bfc8-cd01cd83fd84"}, "list_out": {"src": "hda", "id": "2eb14780dee695c1", "uuid": "467173d6-22cb-4b24-bb51-8f26a5df802e"}, "otucorr_out": {"src": "hda", "id": "b45c9a5a1a91fef7", "uuid": "96768362-0f16-467e-a1f0-c16ac37103f2"}, "shared_out": {"src": "hda", "id": "e55896246ae83c97", "uuid": "aa3df8b6-e53a-4272-9b54-ad9ea1192d01"}, "logfile": {"src": "hda", "id": "6b2453e322eb9595", "uuid": "8616c117-8388-4dd3-b29c-05ff2a7ba0e0"}, "constaxonomy_out": {"src": "hda", "id": "91162ef60fa42a9a", "uuid": "4533757c-1612-4751-93a4-4493befbac61"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.otus(list=list.dat,accnos=accnos.dat)\nYou did not provide a label, I will use the first label in your inputfile.\nSelected 3 OTUs from your list file.\n\nOutput File Names: \nlist.unique.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1196.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1197.dat' list.dat &&  echo 'get.otus( list=list.dat, accnos=accnos.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:37:00.894116", "params": {"corraxes": "null", "dbkey": "\"hg17\"", "otucorr": "null", "shared": "null", "labelsource": "{\"source\": \"list\", \"__current_case__\": 0, \"label\": null}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "constaxonomy": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20339", "id": "8ea35917f4649fec", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_otus.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"shared": {"src": "hda", "id": "76e195bd5a51c206"}, "labelsource|source": "shared", "accnos": {"src": "hda", "id": "597e90101763a05b"}, "labelsource|label": "0.03", "otucorr": {"src": "hda", "id": "7b95a997d2449dc0"}}, "job": {"inputs": {"shared": {"src": "hda", "id": "76e195bd5a51c206", "uuid": "89b37eef-3f9d-44e8-b962-d417da74c0d3"}, "accnos": {"src": "hda", "id": "597e90101763a05b", "uuid": "4d8dcce9-2afb-46b9-a0bf-d2f9fc7902a3"}, "otucorr": {"src": "hda", "id": "7b95a997d2449dc0", "uuid": "3ae2a72b-67e5-45c3-8539-c18b18baafaf"}}, "update_time": "2018-02-08T17:37:28.977887", "tool_id": "mothur_get_otus", "outputs": {"corraxes_out": {"src": "hda", "id": "9b61f34308fff2a9", "uuid": "f4b163d2-98cf-4b7e-8a3f-84e696308c4e"}, "list_out": {"src": "hda", "id": "51ff028a9c4e3d38", "uuid": "b0869f4c-8a97-4ea5-b3cb-b3a0f20cdf57"}, "otucorr_out": {"src": "hda", "id": "3f123558ac7162f4", "uuid": "39faed66-bef0-4e98-9a53-7e94365d63d8"}, "shared_out": {"src": "hda", "id": "c72e590e45abaffd", "uuid": "2cc58074-9cb0-44cd-b0d1-ea5b2b8ae892"}, "logfile": {"src": "hda", "id": "93c45a4fc85043cc", "uuid": "1cb7ccc9-5e1f-43b1-a078-fc434a62be91"}, "constaxonomy_out": {"src": "hda", "id": "5c870d3cd8d2cd2b", "uuid": "cb9391ce-9aa3-4410-b96c-b738f4a7f411"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.otus(shared=shared.dat,otucorr=otucorr.dat,accnos=accnos.dat,label= \r0.03)\nSelected 3 lines from your otu.corr file.\nSelected 3 OTUs from your shared file.\n\nOutput File Names: \notucorr.pick.dat\nshared.0.03.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1204.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1205.dat' shared.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1206.dat' otucorr.dat &&  echo 'get.otus( shared=shared.dat, otucorr=otucorr.dat, accnos=accnos.dat ,label=0.03 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:37:25.632339", "params": {"list": "null", "corraxes": "null", "dbkey": "\"hg17\"", "labelsource": "{\"source\": \"shared\", \"__current_case__\": 1, \"label\": \"0.03\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "constaxonomy": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20469", "id": "86fc1a32b14d4612", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_otus.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "bfb8462f158178af"}, "label": ["0.03", "0.05"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "bfb8462f158178af", "uuid": "9e10e7f7-f01c-4af2-8418-74c67d0e372d"}}, "update_time": "2018-02-08T17:37:46.140219", "tool_id": "mothur_get_rabund", "outputs": {"rabund": {"src": "hda", "id": "14ea0e9326ca1861", "uuid": "f9b65b0c-d862-4482-8b97-9fcf8bdb3d34"}, "logfile": {"src": "hda", "id": "697f459f9324ea39", "uuid": "0903f896-82ca-499b-8cf4-eb4d3fa25238"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.rabund(label=0.03-0.05,sabund=otu.dat,sorted=false)\n0.03\n0.05\n\nOutput File Names: \notu.rabund\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1213.dat' otu.dat &&  echo 'get.rabund( label=0.03-0.05, sabund=otu.dat, sorted=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:37:43.011652", "params": {"count": "null", "sorted": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20564", "id": "c2096fa94981c9cc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_rabund.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "e852cf3dc3c7e42b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "e852cf3dc3c7e42b", "uuid": "3b0701b3-41ab-4ddf-baaa-062ab5dcc4c4"}}, "update_time": "2018-02-08T17:38:03.722756", "tool_id": "mothur_get_rabund", "outputs": {"rabund": {"src": "hda", "id": "8bd0850a7e2f437b", "uuid": "9f88f7ab-3e6a-4d36-8fb7-b6d03ce3ef1a"}, "logfile": {"src": "hda", "id": "0d4414093f575fd4", "uuid": "5172947e-b101-420f-a161-b848fcbf0d4c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.rabund(list=otu.dat,sorted=false)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.rabund\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1216.dat' otu.dat &&  echo 'get.rabund( list=otu.dat, sorted=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:38:00.608880", "params": {"count": "null", "sorted": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20651", "id": "aa6cc630da5109fb", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_rabund.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "081df3333d4f9bbc"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "081df3333d4f9bbc", "uuid": "1b3a0577-d92e-424c-9c76-386b46161f6c"}}, "update_time": "2018-02-08T17:38:21.257992", "tool_id": "mothur_get_relabund", "outputs": {"logfile": {"src": "hda", "id": "782a500b6c6975dc", "uuid": "321e7030-ac8a-42cb-adb1-776f0c471f17"}, "relabund": {"src": "hda", "id": "a99a39c00943ef30", "uuid": "e959a3fd-2378-412e-9001-1150d4439ca4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.relabund(shared=otu.dat,scale=totalgroup)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.relabund\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1219.dat' otu.dat &&  echo 'get.relabund( shared=otu.dat, scale=totalgroup )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:38:18.141836", "params": {"scale": "\"totalgroup\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "null", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20739", "id": "4c469a959b869c08", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_relabund.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "350367f7bcfdf2dd"}, "groups": "forest", "label": ["0.03", "0.05", "0.22"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "350367f7bcfdf2dd", "uuid": "5c37e7ee-4648-49dc-b771-adc2e70fe1cd"}}, "update_time": "2018-02-08T17:38:38.840628", "tool_id": "mothur_get_relabund", "outputs": {"logfile": {"src": "hda", "id": "3819ce922fdcf9e5", "uuid": "707f17eb-240b-45df-afe9-ce959eeaeeef"}, "relabund": {"src": "hda", "id": "41db60f4cf5f2831", "uuid": "07b85144-a45d-494e-a79f-071c71396902"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.relabund(shared=otu.dat,label=0.03-0.05-0.22,groups=forest,scale=to \rtalgroup)\n0.03\n0.05\n0.22\n\nOutput File Names: \notu.relabund\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1222.dat' otu.dat &&  echo 'get.relabund( shared=otu.dat, label=0.03-0.05-0.22, groups=forest, scale=totalgroup )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:38:35.746126", "params": {"scale": "\"totalgroup\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "\"forest\"", "label": "[\"0.03\", \"0.05\", \"0.22\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20829", "id": "3d5f803521123c6e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_relabund.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "8a4ff393c0f15cf9"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "8a4ff393c0f15cf9", "uuid": "ec1c0799-83fe-4d5a-9068-6835c6412863"}}, "update_time": "2018-02-08T17:38:56.557586", "tool_id": "mothur_get_sabund", "outputs": {"logfile": {"src": "hda", "id": "d0f68e425dbbc775", "uuid": "ad4bd606-afc2-4016-9ce2-47640ddef2e0"}, "sabund": {"src": "hda", "id": "2fe4b83a9267275d", "uuid": "e734f708-7b0f-4796-b0ab-9a6890e53b30"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sabund(rabund=otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.sabund\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1225.dat' otu.dat && ln -s 'None' count.dat &&  echo 'get.sabund( rabund=otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:38:53.435236", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "20916", "id": "ec0fb831200675f4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sabund.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "a0a2ae0841f1568c"}, "label": ["0.03", "0.05"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "a0a2ae0841f1568c", "uuid": "7ed19e3e-c6bb-435f-bb82-90d8c7b36cdd"}}, "update_time": "2018-02-08T17:39:14.113078", "tool_id": "mothur_get_sabund", "outputs": {"logfile": {"src": "hda", "id": "24da0eeb3eec1daa", "uuid": "c1698ca0-1cde-4dd4-a1ca-fc3d5d5626a8"}, "sabund": {"src": "hda", "id": "3f9f964fe6121e92", "uuid": "8e27ffcb-96a8-490d-b26c-61861a529567"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sabund(label=0.03-0.05,list=otu.dat)\n0.03\n0.05\n\nOutput File Names: \notu.sabund\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1228.dat' otu.dat && ln -s 'None' count.dat &&  echo 'get.sabund( label=0.03-0.05, list=otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:39:11.000346", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21004", "id": "f1f75462f416e186", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sabund.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"accnos": {"src": "hda", "id": "61d69f53aecda797"}, "fasta_in": {"src": "hda", "id": "c58efa153eba9565"}, "dups": false}, "job": {"inputs": {"accnos": {"src": "hda", "id": "61d69f53aecda797", "uuid": "ee95bfe3-7425-4e29-806a-84a726cab72c"}, "fasta_in": {"src": "hda", "id": "c58efa153eba9565", "uuid": "f541b4af-c928-4167-8bfd-84236cc32cb3"}}, "update_time": "2018-02-08T17:39:34.986176", "tool_id": "mothur_get_seqs", "outputs": {"logfile": {"src": "hda", "id": "5e3a9652455a7ed3", "uuid": "3b977c88-368c-44a6-940c-2d5b765bfe9e"}, "fasta_out": {"src": "hda", "id": "631e6f3f808d1daa", "uuid": "f7c805f9-9e85-41bb-b789-56c2b8e433b9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.seqs(accnos=accnos.dat,fasta=fasta_in.dat,dups=false)\nSelected 3 sequences from your fasta file.\n\nOutput File Names: \nfasta_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1231.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1232.dat' fasta_in.dat && ln -s 'None' fastq_in.dat && ln -s 'None' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat &&  echo 'get.seqs( accnos=accnos.dat, fasta=fasta_in.dat, dups=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:39:31.864369", "params": {"fastq_in": "null", "dups": "\"false\"", "count_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21125", "id": "f3e7443ed4070d7c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fastq_in": {"src": "hda", "id": "011edc069103d7ec"}, "accnos": {"src": "hda", "id": "96df66444a6ec901"}}, "job": {"inputs": {"fastq_in": {"src": "hda", "id": "011edc069103d7ec", "uuid": "2a4e4303-b583-4bb7-8dc3-090ac8d784fb"}, "accnos": {"src": "hda", "id": "96df66444a6ec901", "uuid": "5f09f2d8-e815-481e-8319-680abfc1ee55"}}, "update_time": "2018-02-08T17:39:50.405005", "tool_id": "mothur_get_seqs", "outputs": {"logfile": {"src": "hda", "id": "11e2f427f678fd46", "uuid": "c8919f6f-d45e-476c-b870-02cd51988a1e"}, "fastq_out": {"src": "hda", "id": "aecf4c8180e80a4e", "uuid": "ebc254ae-cb1a-41b9-9b0d-dba079754227"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.seqs(accnos=accnos.dat,fastq=fastq_in.dat,dups=dups)\nSelected 3 sequences from your fastq file.\n\nOutput File Names: \nfastq_in.pick.dat\n\n[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1235.dat' accnos.dat && ln -s 'None' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1236.dat' fastq_in.dat && ln -s 'None' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat &&  echo 'get.seqs( accnos=accnos.dat, fastq=fastq_in.dat, dups=dups )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:39:47.449707", "params": {"dups": "\"true\"", "fasta_in": "null", "count_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21248", "id": "a5170ff908b4401b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fastq_in": {"src": "hda", "id": "f34bcbdd0a72e0b4"}, "accnos": {"src": "hda", "id": "429998073c64a880"}, "fasta_in": {"src": "hda", "id": "ae159bf1c2125429"}, "dups": false}, "job": {"inputs": {"fastq_in": {"src": "hda", "id": "f34bcbdd0a72e0b4", "uuid": "d71804cd-863d-4cf8-9f8e-12a37d7ec74c"}, "fasta_in": {"src": "hda", "id": "ae159bf1c2125429", "uuid": "fd50d748-91bc-4253-b3a7-57b119542771"}, "accnos": {"src": "hda", "id": "429998073c64a880", "uuid": "ff206f5a-eecf-4f9d-9f49-88d2a2c7f8e8"}}, "update_time": "2018-02-08T17:40:10.037647", "tool_id": "mothur_get_seqs", "outputs": {"fasta_out": {"src": "hda", "id": "cc004dc337e74e6b", "uuid": "ec9de38c-7807-4109-aaac-4e2422131fd7"}, "logfile": {"src": "hda", "id": "38134c7758ca35f5", "uuid": "d334d6cc-a785-427d-b0e3-653a1cee3dc4"}, "fastq_out": {"src": "hda", "id": "a0e87d70eb117c6b", "uuid": "bb5beb8c-57ac-4fb0-8a64-98519ef3e355"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.seqs(accnos=accnos.dat,fasta=fasta_in.dat,fastq=fastq_in.dat,dups=f \ralse)\nSelected 3 sequences from your fasta file.\nSelected 3 sequences from your fastq file.\n\nOutput File Names: \nfasta_in.pick.dat\nfastq_in.pick.dat\n\n[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1239.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1240.dat' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1241.dat' fastq_in.dat && ln -s 'None' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat &&  echo 'get.seqs( accnos=accnos.dat, fasta=fasta_in.dat, fastq=fastq_in.dat, dups=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:40:06.074352", "params": {"dups": "\"false\"", "count_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21397", "id": "2b49763c55874680", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"accnos": {"src": "hda", "id": "2af669c98ffba1bc"}, "count_in": {"src": "hda", "id": "28ef132ecd41da41"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "2af669c98ffba1bc", "uuid": "495fec17-107e-4eee-8610-1c4e96f58a6d"}, "count_in": {"src": "hda", "id": "28ef132ecd41da41", "uuid": "f7cdf3dd-535d-4b35-883b-54caf42d9374"}}, "update_time": "2018-02-08T17:40:27.491400", "tool_id": "mothur_get_seqs", "outputs": {"logfile": {"src": "hda", "id": "7ccd0d003f1c770e", "uuid": "2b67b8c6-c764-4f46-ae9b-fe8bec450035"}, "count_out": {"src": "hda", "id": "0a69fafee8fab989", "uuid": "00faa3ff-4c97-424a-b5ef-5abf56f80208"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.seqs(accnos=accnos.dat,count=count_in.dat,dups=dups)\nSelected 8 sequences from your count file.\n\nOutput File Names: \ncount_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1245.dat' accnos.dat && ln -s 'None' fasta_in.dat && ln -s 'None' fastq_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1246.dat' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat &&  echo 'get.seqs( accnos=accnos.dat, count=count_in.dat, dups=dups )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:40:24.388969", "params": {"fastq_in": "null", "dups": "\"true\"", "fasta_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21528", "id": "a5b8d21ac8fc30ea", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"infile|intype": "in_shared", "infile|otu": {"src": "hda", "id": "8991ff1b69b89ded"}, "infile|seqsfrom|selection": "shared"}, "job": {"inputs": {"otu": {"src": "hda", "id": "8991ff1b69b89ded", "uuid": "872bf3b7-9f50-4f08-8cae-3392147d7120"}}, "update_time": "2018-02-08T17:40:42.546493", "tool_id": "mothur_get_sharedseqs", "outputs": {"__new_primary_file_0.55.unique.forest_pasture|0.01.unique.forest_pasture__": {"src": "hda", "id": "fe96fd381a33cce5", "uuid": "6e62e8a0-9565-42a2-9211-7f4045d9802e"}, "__new_primary_file_0.55.unique.forest_pasture|0.03.unique.forest_pasture__": {"src": "hda", "id": "abbd1960cbf160f9", "uuid": "03fd6ca0-4f2c-465a-8cb8-dbe825c563f1"}, "__new_primary_file_0.55.unique.forest_pasture|0.12.unique.forest_pasture__": {"src": "hda", "id": "d07b459d41c7c945", "uuid": "03f90a30-0551-4910-97a7-dc0c226679fb"}, "__new_primary_file_0.55.unique.forest_pasture|0.08.unique.forest_pasture__": {"src": "hda", "id": "0bb3941465c9f795", "uuid": "5c0613c1-f9a1-484d-a2b3-26a54e649ee9"}, "__new_primary_file_0.55.unique.forest_pasture|0.36.unique.forest_pasture__": {"src": "hda", "id": "c785bef273d68b1e", "uuid": "1b0a9c63-56b9-4972-8b9f-02ba5c02c04f"}, "__new_primary_file_0.55.unique.forest_pasture|0.33.unique.forest_pasture__": {"src": "hda", "id": "696fb5296f68042e", "uuid": "271c55c4-3601-4cfa-8890-aa71391cd4e4"}, "__new_primary_file_0.55.unique.forest_pasture|0.23.unique.forest_pasture__": {"src": "hda", "id": "1705da10f105bf38", "uuid": "95d04c9c-0972-45cb-81b3-61f008596f88"}, "__new_primary_file_0.55.unique.forest_pasture|0.32.unique.forest_pasture__": {"src": "hda", "id": "94b2b05bccf8c5b7", "uuid": "f0f831e2-5c81-40f5-af81-a6174cf1a4e5"}, "__new_primary_file_0.55.unique.forest_pasture|0.06.unique.forest_pasture__": {"src": "hda", "id": "ee43e48dbb3db358", "uuid": "a4e1ae3d-6947-49bb-8b50-ab5d37eacbea"}, "__new_primary_file_0.55.unique.forest_pasture|0.45.unique.forest_pasture__": {"src": "hda", "id": "e959a6a79feb9b78", "uuid": "860cb981-ff58-4f47-ba3f-7859fb678339"}, "__new_primary_file_0.55.unique.forest_pasture|0.38.unique.forest_pasture__": {"src": "hda", "id": "af849d2a7341fcce", "uuid": "68ec2522-535a-423f-89de-ac8ee8073ae1"}, "__new_primary_file_0.55.unique.forest_pasture|0.04.unique.forest_pasture__": {"src": "hda", "id": "e1caecba7fa68b40", "uuid": "038e3223-f87e-4d54-b647-e80c270d7fde"}, "__new_primary_file_0.55.unique.forest_pasture|0.20.unique.forest_pasture__": {"src": "hda", "id": "93d3f7925ba4d071", "uuid": "b43ed593-75eb-4c3f-bfda-2a684feb05d9"}, "__new_primary_file_0.55.unique.forest_pasture|0.26.unique.forest_pasture__": {"src": "hda", "id": "98949929b1176202", "uuid": "7b478ce3-2d42-4a2f-b821-11a03d939363"}, "__new_primary_file_0.55.unique.forest_pasture|0.15.unique.forest_pasture__": {"src": "hda", "id": "c3ce2a80c0d89459", "uuid": "92173f88-ce59-4d94-96f8-4eb3b91721df"}, "__new_primary_file_0.55.unique.forest_pasture|0.02.unique.forest_pasture__": {"src": "hda", "id": "2114951d23217870", "uuid": "30bbdd45-8509-476d-8500-7fb15c01fbfc"}, "__new_primary_file_0.55.unique.forest_pasture|0.10.unique.forest_pasture__": {"src": "hda", "id": "5f161a30c8b2f408", "uuid": "9dc304f3-b581-4555-b2f0-4fcc85d063a6"}, "__new_primary_file_0.55.unique.forest_pasture|0.17.unique.forest_pasture__": {"src": "hda", "id": "b9bb71cf44c7a0e7", "uuid": "cddaf8f8-e410-4633-aa7a-2bbec88cbc5c"}, "__new_primary_file_0.55.unique.forest_pasture|0.29.unique.forest_pasture__": {"src": "hda", "id": "b4a250cf71b57d6e", "uuid": "06f5481a-e0b3-479a-8508-9a91fc743a7a"}, "__new_primary_file_0.55.unique.forest_pasture|0.09.unique.forest_pasture__": {"src": "hda", "id": "22ee6ec8bba94753", "uuid": "7c493108-e4fa-4a7e-bb29-e20ede7859ab"}, "__new_primary_file_0.55.unique.forest_pasture|0.22.unique.forest_pasture__": {"src": "hda", "id": "e79f5a70b4d84628", "uuid": "98be88e4-5708-41e8-ac3d-b8d99af0623f"}, "__new_primary_file_0.55.unique.forest_pasture|0.16.unique.forest_pasture__": {"src": "hda", "id": "c0880ab75f60a05d", "uuid": "d1962c02-1150-42c4-a0b5-53f95b28f23b"}, "__new_primary_file_0.55.unique.forest_pasture|0.14.unique.forest_pasture__": {"src": "hda", "id": "ae5dfc6c4ccf9fa5", "uuid": "440852d5-6a57-4390-beca-0da217e15cb3"}, "__new_primary_file_0.55.unique.forest_pasture|0.05.unique.forest_pasture__": {"src": "hda", "id": "39ba608ca28de802", "uuid": "c5226c97-5550-4504-9368-9c34d154f7a0"}, "__new_primary_file_0.55.unique.forest_pasture|0.19.unique.forest_pasture__": {"src": "hda", "id": "c8711b8e31575185", "uuid": "e388917c-c66e-4775-a573-6876087759ce"}, "__new_primary_file_0.55.unique.forest_pasture|0.27.unique.forest_pasture__": {"src": "hda", "id": "a14db3cd22562c1c", "uuid": "facbec9c-ef23-4a49-832e-cb72d88e40c3"}, "__new_primary_file_0.55.unique.forest_pasture|0.25.unique.forest_pasture__": {"src": "hda", "id": "fb26921841cf93b6", "uuid": "4a208dfa-fb3b-406b-a7ec-1ebd75312147"}, "__new_primary_file_0.55.unique.forest_pasture|0.21.unique.forest_pasture__": {"src": "hda", "id": "a53b61a2057d1d37", "uuid": "2b481e20-a397-492d-8c8e-4ae5e926d273"}, "__new_primary_file_0.55.unique.forest_pasture|0.11.unique.forest_pasture__": {"src": "hda", "id": "a2b4f906be8b27da", "uuid": "2d894fec-a661-443b-91f8-63eedcc74c30"}, "__new_primary_file_0.55.unique.forest_pasture|0.41.unique.forest_pasture__": {"src": "hda", "id": "3c94cd72eddabd04", "uuid": "4b0ad5ec-65dc-4e5f-acb3-836c68d942dd"}, "__new_primary_file_0.55.unique.forest_pasture|0.13.unique.forest_pasture__": {"src": "hda", "id": "81cefc9a8787c281", "uuid": "20a466e5-907c-40b2-97dc-aad52b3b7197"}, "__new_primary_file_0.55.unique.forest_pasture|0.55.unique.forest_pasture__": {"src": "hda", "id": "f9dbbadeec4a7667", "uuid": "d64b8575-454c-4727-ad23-b5d8c6fe59ca"}, "logfile": {"src": "hda", "id": "97dddce84ce4448e", "uuid": "42368fb8-aa6a-44b7-9809-9ca33a75f9a0"}, "__new_primary_file_0.55.unique.forest_pasture|0.24.unique.forest_pasture__": {"src": "hda", "id": "f4069f60e8f3e4ae", "uuid": "5a3e0161-4ff4-402f-9c1a-b5d52d8c353c"}, "__new_primary_file_0.55.unique.forest_pasture|0.07.unique.forest_pasture__": {"src": "hda", "id": "18db42ecae15c51a", "uuid": "92fd9874-876c-4b24-9dad-7a4a10b4177a"}, "__new_primary_file_0.55.unique.forest_pasture|0.18.unique.forest_pasture__": {"src": "hda", "id": "0bc713a3d3ce28f8", "uuid": "c8092fa4-b78d-4f24-acf5-7d3518cf5467"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sharedseqs(shared=infile_otu.dat)\nunique\t0 - No otus shared by groups  forest  pasture.\n0.01\t1\n0.02\t1\n0.03\t2\n0.04\t4\n0.05\t7\n0.06\t9\n0.07\t9\n0.08\t9\n0.09\t9\n0.10\t8\n0.11\t8\n0.12\t8\n0.13\t8\n0.14\t9\n0.15\t9\n0.16\t9\n0.17\t10\n0.18\t10\n0.19\t11\n0.20\t10\n0.21\t9\n0.22\t9\n0.23\t8\n0.24\t7\n0.25\t7\n0.26\t7\n0.27\t6\n0.29\t4\n0.32\t3\n0.33\t2\n0.36\t2\n0.38\t2\n0.41\t1\n0.45\t1\n0.55\t1\n\nOutput File Names: \ninfile_otu.0.01.unique.forest_pasture.shared.seqs\ninfile_otu.0.02.unique.forest_pasture.shared.seqs\ninfile_otu.0.03.unique.forest_pasture.shared.seqs\ninfile_otu.0.04.unique.forest_pasture.shared.seqs\ninfile_otu.0.05.unique.forest_pasture.shared.seqs\ninfile_otu.0.06.unique.forest_pasture.shared.seqs\ninfile_otu.0.07.unique.forest_pasture.shared.seqs\ninfile_otu.0.08.unique.forest_pasture.shared.seqs\ninfile_otu.0.09.unique.forest_pasture.shared.seqs\ninfile_otu.0.10.unique.forest_pasture.shared.seqs\ninfile_otu.0.11.unique.forest_pasture.shared.seqs\ninfile_otu.0.12.unique.forest_pasture.shared.seqs\ninfile_otu.0.13.unique.forest_pasture.shared.seqs\ninfile_otu.0.14.unique.forest_pasture.shared.seqs\ninfile_otu.0.15.unique.forest_pasture.shared.seqs\ninfile_otu.0.16.unique.forest_pasture.shared.seqs\ninfile_otu.0.17.unique.forest_pasture.shared.seqs\ninfile_otu.0.18.unique.forest_pasture.shared.seqs\ninfile_otu.0.19.unique.forest_pasture.shared.seqs\ninfile_otu.0.20.unique.forest_pasture.shared.seqs\ninfile_otu.0.21.unique.forest_pasture.shared.seqs\ninfile_otu.0.22.unique.forest_pasture.shared.seqs\ninfile_otu.0.23.unique.forest_pasture.shared.seqs\ninfile_otu.0.24.unique.forest_pasture.shared.seqs\ninfile_otu.0.25.unique.forest_pasture.shared.seqs\ninfile_otu.0.26.unique.forest_pasture.shared.seqs\ninfile_otu.0.27.unique.forest_pasture.shared.seqs\ninfile_otu.0.29.unique.forest_pasture.shared.seqs\ninfile_otu.0.32.unique.forest_pasture.shared.seqs\ninfile_otu.0.33.unique.forest_pasture.shared.seqs\ninfile_otu.0.36.unique.forest_pasture.shared.seqs\ninfile_otu.0.38.unique.forest_pasture.shared.seqs\ninfile_otu.0.41.unique.forest_pasture.shared.seqs\ninfile_otu.0.45.unique.forest_pasture.shared.seqs\ninfile_otu.0.55.unique.forest_pasture.shared.seqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1249.dat' infile_otu.dat &&  echo 'get.sharedseqs( shared=infile_otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:40:37.022378", "params": {"output": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"seqsfrom\": {\"selection\": \"shared\", \"groups\": null, \"__current_case__\": 1}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1249}]}, \"__current_case__\": 0, \"label\": null}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21699", "id": "84069f8e0a4c5a8e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sharedseqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"infile|intype": "in_listgroup", "infile|otu": {"src": "hda", "id": "4b7d958e0a57cf76"}, "infile|group": {"src": "hda", "id": "22e37d6ba86e2a2e"}}, "job": {"inputs": {"group": {"src": "hda", "id": "22e37d6ba86e2a2e", "uuid": "57e7e54e-4d04-466e-aee7-80aab3ddf238"}, "otu": {"src": "hda", "id": "4b7d958e0a57cf76", "uuid": "094a5b5c-cacc-4fa3-bb7d-4cdd0535c932"}}, "update_time": "2018-02-08T17:41:06.572855", "tool_id": "mothur_get_sharedseqs", "outputs": {"__new_primary_file_0.55.unique.forest_pasture|0.01.unique.forest_pasture__": {"src": "hda", "id": "a6e53d78c2aa075a", "uuid": "30f325e4-4f11-4b7d-bde7-36f0f667cfa3"}, "__new_primary_file_0.55.unique.forest_pasture|0.03.unique.forest_pasture__": {"src": "hda", "id": "e129f12cdcbea9f8", "uuid": "6bbf9fcb-96d3-4ae7-b4a5-ab6216cc6e48"}, "__new_primary_file_0.55.unique.forest_pasture|0.12.unique.forest_pasture__": {"src": "hda", "id": "993d97a54f58371d", "uuid": "393135e9-fa41-4153-9aa3-2660c092c92c"}, "__new_primary_file_0.55.unique.forest_pasture|0.08.unique.forest_pasture__": {"src": "hda", "id": "87221f8fb11b5cc8", "uuid": "9c6f73d1-4c93-40cb-8252-899acd0218a6"}, "__new_primary_file_0.55.unique.forest_pasture|0.36.unique.forest_pasture__": {"src": "hda", "id": "983b943d65d6c7d7", "uuid": "e0b99c1d-e30f-4277-bf5c-f419f0638f89"}, "__new_primary_file_0.55.unique.forest_pasture|0.33.unique.forest_pasture__": {"src": "hda", "id": "1c22c17396d9a02a", "uuid": "4196bbee-376f-4c74-b415-d84fb2253cea"}, "__new_primary_file_0.55.unique.forest_pasture|0.23.unique.forest_pasture__": {"src": "hda", "id": "f39de65e2034ed3a", "uuid": "c79dcaf1-76cf-4441-981b-f6a2c2d1aef4"}, "__new_primary_file_0.55.unique.forest_pasture|0.32.unique.forest_pasture__": {"src": "hda", "id": "c8f16105fabce55c", "uuid": "5dffad01-87c3-4695-a705-cf92f638cffb"}, "__new_primary_file_0.55.unique.forest_pasture|0.06.unique.forest_pasture__": {"src": "hda", "id": "35de84ce53a9c828", "uuid": "4ba701d9-96ce-476d-9d70-091352681b8f"}, "__new_primary_file_0.55.unique.forest_pasture|0.45.unique.forest_pasture__": {"src": "hda", "id": "9d80b37e646651a2", "uuid": "cca381a8-f0b1-451f-a0ca-4e21ff97a0ce"}, "__new_primary_file_0.55.unique.forest_pasture|0.38.unique.forest_pasture__": {"src": "hda", "id": "1f5f52e2309ff559", "uuid": "d706fac0-066c-4140-a107-93c7a7dadc7b"}, "__new_primary_file_0.55.unique.forest_pasture|0.04.unique.forest_pasture__": {"src": "hda", "id": "914cc9e62ef5365f", "uuid": "d748bcde-2616-4fe2-8ba0-70fc5002f414"}, "__new_primary_file_0.55.unique.forest_pasture|0.20.unique.forest_pasture__": {"src": "hda", "id": "fad0ab3aea5cc191", "uuid": "23e411ec-733c-4172-b226-749c7bcc3a3b"}, "__new_primary_file_0.55.unique.forest_pasture|0.26.unique.forest_pasture__": {"src": "hda", "id": "6b853ad1a5dc9670", "uuid": "d152f781-531f-4064-ac9e-77870a5fad59"}, "__new_primary_file_0.55.unique.forest_pasture|0.15.unique.forest_pasture__": {"src": "hda", "id": "5b7a47d04f2ce92e", "uuid": "e272186f-af71-4f73-931c-caf7ff00bb2b"}, "__new_primary_file_0.55.unique.forest_pasture|0.02.unique.forest_pasture__": {"src": "hda", "id": "fde35c4f1f75764c", "uuid": "21a7781c-a131-4cb1-9782-18fd7c7f2ae3"}, "__new_primary_file_0.55.unique.forest_pasture|0.10.unique.forest_pasture__": {"src": "hda", "id": "c3e3c95393385769", "uuid": "8f838ca7-cb0a-49ed-92a0-7af2587aa95a"}, "__new_primary_file_0.55.unique.forest_pasture|0.17.unique.forest_pasture__": {"src": "hda", "id": "bd17947ec32bf83e", "uuid": "cc13beef-971d-43d5-b420-278a82c15ab7"}, "__new_primary_file_0.55.unique.forest_pasture|0.29.unique.forest_pasture__": {"src": "hda", "id": "89f023fa51ac47b1", "uuid": "e3ec40de-c3d1-4752-a9b1-eaa6a8c5df14"}, "__new_primary_file_0.55.unique.forest_pasture|0.09.unique.forest_pasture__": {"src": "hda", "id": "e87af5eb583a6a0d", "uuid": "60bb585e-a501-4162-a97e-a817c7190865"}, "__new_primary_file_0.55.unique.forest_pasture|0.22.unique.forest_pasture__": {"src": "hda", "id": "eef93538df20bc17", "uuid": "5a98686b-b17a-412a-8304-bcf4cb4d7a3d"}, "__new_primary_file_0.55.unique.forest_pasture|0.16.unique.forest_pasture__": {"src": "hda", "id": "bdaadc18ac151cd2", "uuid": "4595f913-1a6d-402a-bc6e-db035606e6c5"}, "__new_primary_file_0.55.unique.forest_pasture|0.14.unique.forest_pasture__": {"src": "hda", "id": "461683b0bc43792a", "uuid": "7c11441b-93c0-440a-bd46-3d9a53018f5a"}, "__new_primary_file_0.55.unique.forest_pasture|0.05.unique.forest_pasture__": {"src": "hda", "id": "ad58d1ed1e353fc6", "uuid": "28520fde-77ab-44e6-a2b3-975f4aa7024d"}, "__new_primary_file_0.55.unique.forest_pasture|0.19.unique.forest_pasture__": {"src": "hda", "id": "f8b18a16ce2a2213", "uuid": "26ed470f-185b-429e-8f93-f995c357df9d"}, "__new_primary_file_0.55.unique.forest_pasture|0.27.unique.forest_pasture__": {"src": "hda", "id": "b45a8ae42a18587e", "uuid": "59e2a1d6-bb25-439e-9308-b5a96a05b7de"}, "__new_primary_file_0.55.unique.forest_pasture|0.25.unique.forest_pasture__": {"src": "hda", "id": "0534db83ede63e64", "uuid": "be926160-a075-45d4-ad37-46cbf886ed43"}, "__new_primary_file_0.55.unique.forest_pasture|0.21.unique.forest_pasture__": {"src": "hda", "id": "9a87b669ba9ab9db", "uuid": "d4f58cdd-b711-400e-a76e-0cda681abfd8"}, "__new_primary_file_0.55.unique.forest_pasture|0.11.unique.forest_pasture__": {"src": "hda", "id": "e2e4c35d5ff4266b", "uuid": "12a6ac0f-1db6-4b96-875a-fcb7009814f4"}, "__new_primary_file_0.55.unique.forest_pasture|0.41.unique.forest_pasture__": {"src": "hda", "id": "220fe64dce861a50", "uuid": "c057e845-b61a-4d4c-bb84-90eb7387d194"}, "__new_primary_file_0.55.unique.forest_pasture|0.13.unique.forest_pasture__": {"src": "hda", "id": "64d82fdd6e113cc6", "uuid": "f10dd2e4-d8e1-4baa-9451-3d5d9bc74197"}, "__new_primary_file_0.55.unique.forest_pasture|0.55.unique.forest_pasture__": {"src": "hda", "id": "cca4740627632b2c", "uuid": "7dd79344-3624-4f33-99e7-040a5fe90020"}, "logfile": {"src": "hda", "id": "76f3dabcdd118837", "uuid": "134d204a-412b-4b70-98a3-76345bf064c8"}, "__new_primary_file_0.55.unique.forest_pasture|0.24.unique.forest_pasture__": {"src": "hda", "id": "eb651194166b0289", "uuid": "a6ed694b-7c67-4583-8274-10269dabae15"}, "__new_primary_file_0.55.unique.forest_pasture|0.07.unique.forest_pasture__": {"src": "hda", "id": "a552f60ce7ee1aa3", "uuid": "799d8b21-d71e-4298-8675-6b790f0b7e06"}, "__new_primary_file_0.55.unique.forest_pasture|0.18.unique.forest_pasture__": {"src": "hda", "id": "8c4aac77b9acb762", "uuid": "92b51647-e348-4bb0-988f-91020a0076da"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sharedseqs(list=infile_otu.dat,group=infile.group.dat)\nunique\t0 - No otus shared by groups  forest  pasture.\n0.01\t1\n0.02\t1\n0.03\t2\n0.04\t4\n0.05\t7\n0.06\t9\n0.07\t9\n0.08\t9\n0.09\t9\n0.10\t8\n0.11\t8\n0.12\t8\n0.13\t8\n0.14\t9\n0.15\t9\n0.16\t9\n0.17\t10\n0.18\t10\n0.19\t11\n0.20\t10\n0.21\t9\n0.22\t9\n0.23\t8\n0.24\t7\n0.25\t7\n0.26\t7\n0.27\t6\n0.29\t4\n0.32\t3\n0.33\t2\n0.36\t2\n0.38\t2\n0.41\t1\n0.45\t1\n0.55\t1\n\nOutput File Names: \ninfile_otu.0.01.unique.forest_pasture.shared.seqs\ninfile_otu.0.02.unique.forest_pasture.shared.seqs\ninfile_otu.0.03.unique.forest_pasture.shared.seqs\ninfile_otu.0.04.unique.forest_pasture.shared.seqs\ninfile_otu.0.05.unique.forest_pasture.shared.seqs\ninfile_otu.0.06.unique.forest_pasture.shared.seqs\ninfile_otu.0.07.unique.forest_pasture.shared.seqs\ninfile_otu.0.08.unique.forest_pasture.shared.seqs\ninfile_otu.0.09.unique.forest_pasture.shared.seqs\ninfile_otu.0.10.unique.forest_pasture.shared.seqs\ninfile_otu.0.11.unique.forest_pasture.shared.seqs\ninfile_otu.0.12.unique.forest_pasture.shared.seqs\ninfile_otu.0.13.unique.forest_pasture.shared.seqs\ninfile_otu.0.14.unique.forest_pasture.shared.seqs\ninfile_otu.0.15.unique.forest_pasture.shared.seqs\ninfile_otu.0.16.unique.forest_pasture.shared.seqs\ninfile_otu.0.17.unique.forest_pasture.shared.seqs\ninfile_otu.0.18.unique.forest_pasture.shared.seqs\ninfile_otu.0.19.unique.forest_pasture.shared.seqs\ninfile_otu.0.20.unique.forest_pasture.shared.seqs\ninfile_otu.0.21.unique.forest_pasture.shared.seqs\ninfile_otu.0.22.unique.forest_pasture.shared.seqs\ninfile_otu.0.23.unique.forest_pasture.shared.seqs\ninfile_otu.0.24.unique.forest_pasture.shared.seqs\ninfile_otu.0.25.unique.forest_pasture.shared.seqs\ninfile_otu.0.26.unique.forest_pasture.shared.seqs\ninfile_otu.0.27.unique.forest_pasture.shared.seqs\ninfile_otu.0.29.unique.forest_pasture.shared.seqs\ninfile_otu.0.32.unique.forest_pasture.shared.seqs\ninfile_otu.0.33.unique.forest_pasture.shared.seqs\ninfile_otu.0.36.unique.forest_pasture.shared.seqs\ninfile_otu.0.38.unique.forest_pasture.shared.seqs\ninfile_otu.0.41.unique.forest_pasture.shared.seqs\ninfile_otu.0.45.unique.forest_pasture.shared.seqs\ninfile_otu.0.55.unique.forest_pasture.shared.seqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1286.dat' infile_otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1287.dat' infile.group.dat && ln -s 'None' infile_fasta.dat && ln -s 'None' count_in.dat &&  echo 'get.sharedseqs( list=infile_otu.dat  ,group=infile.group.dat  )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:41:01.432445", "params": {"output": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"group\": {\"values\": [{\"src\": \"hda\", \"id\": 1287}]}, \"intype\": \"in_listgroup\", \"seqsfrom\": {\"selection\": \"all\", \"__current_case__\": 2}, \"count_in\": null, \"label\": null, \"__current_case__\": 1, \"fasta\": null, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1286}]}}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21859", "id": "ec3c9d08d9062ead", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sharedseqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"infile|seqsfrom|groups": ["forest", "pasture"], "infile|intype": "in_shared", "infile|otu": {"src": "hda", "id": "702df83b8d383f91"}, "infile|seqsfrom|selection": "shared", "infile|label": ["0.03", "0.33", "0.41"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "702df83b8d383f91", "uuid": "5f1cc371-ef50-4a1b-a8c9-5f0ddde4d111"}}, "update_time": "2018-02-08T17:41:26.288697", "tool_id": "mothur_get_sharedseqs", "outputs": {"__new_primary_file_0.41.forest_pasture|0.33.forest_pasture__": {"src": "hda", "id": "54f6c1e83cddf017", "uuid": "7fc3b6d7-cb7e-4156-a9a4-c6db5eee51a6"}, "logfile": {"src": "hda", "id": "4520cfd618792d79", "uuid": "83f35ee5-b93d-4d5c-ada4-b251a4b542b2"}, "__new_primary_file_0.41.forest_pasture|0.41.forest_pasture__": {"src": "hda", "id": "a47f21eee894769a", "uuid": "a2ea857a-c68b-47fc-8e4f-5617cbf4906b"}, "__new_primary_file_0.41.forest_pasture|0.03.forest_pasture__": {"src": "hda", "id": "edbb972fe95b9ac8", "uuid": "7ac4d017-b073-481c-bce7-ec153444bc1f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sharedseqs(shared=infile_otu.dat,label=0.03-0.33-0.41,sharedgroups= \rforest-pasture)\n0.03\t2\n0.33\t2\n0.41\t1\n\nOutput File Names: \ninfile_otu.0.03.forest_pasture.shared.seqs\ninfile_otu.0.33.forest_pasture.shared.seqs\ninfile_otu.0.41.forest_pasture.shared.seqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1324.dat' infile_otu.dat &&  echo 'get.sharedseqs( shared=infile_otu.dat ,label=0.03-0.33-0.41 ,sharedgroups=forest-pasture )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:41:23.089850", "params": {"output": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"seqsfrom\": {\"selection\": \"shared\", \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 1}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1324}]}, \"__current_case__\": 0, \"label\": [\"0.03\", \"0.33\", \"0.41\"]}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "21958", "id": "802ffc5c50268813", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sharedseqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"infile|seqsfrom|groups": "pasture", "infile|otu": {"src": "hda", "id": "c8023bd8606946c1"}, "infile|seqsfrom|selection": "unique", "infile|intype": "in_shared"}, "job": {"inputs": {"otu": {"src": "hda", "id": "c8023bd8606946c1", "uuid": "9333bd68-810e-4038-a81c-69f6b19fe400"}}, "update_time": "2018-02-08T17:41:45.507774", "tool_id": "mothur_get_sharedseqs", "outputs": {"__new_primary_file_unique.unique.pasture|0.02.unique.pasture__": {"src": "hda", "id": "3f577f2345e462ae", "uuid": "389726b7-6e66-4f21-af77-918c4fa800ff"}, "__new_primary_file_unique.unique.pasture|0.17.unique.pasture__": {"src": "hda", "id": "1051479745a019c3", "uuid": "b6f6e2d2-8d64-4423-8ba4-de195b2e4b06"}, "__new_primary_file_unique.unique.pasture|0.13.unique.pasture__": {"src": "hda", "id": "d1a9e52845840800", "uuid": "e77a422a-81af-41a8-8cda-c47a4601f4c9"}, "__new_primary_file_unique.unique.pasture|0.16.unique.pasture__": {"src": "hda", "id": "58bf1d0ea28ad39d", "uuid": "6b9687e9-7b07-46af-8b56-7f0575751939"}, "__new_primary_file_unique.unique.pasture|0.07.unique.pasture__": {"src": "hda", "id": "547dde384e3b6a29", "uuid": "b1a80092-fc04-4452-8809-59ed8dbc52b7"}, "__new_primary_file_unique.unique.pasture|0.06.unique.pasture__": {"src": "hda", "id": "fcd56e94d175000a", "uuid": "84b9cd98-591f-4e49-b863-e9077d4387d3"}, "__new_primary_file_unique.unique.pasture|0.32.unique.pasture__": {"src": "hda", "id": "b1f82c5e1406130e", "uuid": "949a768c-0f8b-469b-9593-eb1561dee43a"}, "__new_primary_file_unique.unique.pasture|0.20.unique.pasture__": {"src": "hda", "id": "2dabc8e196f33f11", "uuid": "a5c54946-b5e3-466c-9679-5c2ea79bd37f"}, "__new_primary_file_unique.unique.pasture|0.09.unique.pasture__": {"src": "hda", "id": "c08963815c2b5a83", "uuid": "a01509e5-9712-46e0-befa-b910588c5905"}, "__new_primary_file_unique.unique.pasture|0.22.unique.pasture__": {"src": "hda", "id": "94f70b574060c9d1", "uuid": "ba88e709-5a51-43e1-b653-a65f901202f2"}, "__new_primary_file_unique.unique.pasture|0.18.unique.pasture__": {"src": "hda", "id": "9099f171c3563201", "uuid": "f6e48820-b9a6-4452-bc86-a31e6a55c681"}, "__new_primary_file_unique.unique.pasture|0.41.unique.pasture__": {"src": "hda", "id": "544cc4ca9245289d", "uuid": "4cd8cee7-bd99-43ce-b79f-09a58f6cee55"}, "__new_primary_file_unique.unique.pasture|0.14.unique.pasture__": {"src": "hda", "id": "6038958fffcae8aa", "uuid": "be2077b6-7958-4ca9-bcd2-f7a8f8e874fc"}, "__new_primary_file_unique.unique.pasture|0.12.unique.pasture__": {"src": "hda", "id": "cdf7e255cbf9ad98", "uuid": "1fdca5fb-0bb8-4b2f-9874-4960f3b23105"}, "__new_primary_file_unique.unique.pasture|0.23.unique.pasture__": {"src": "hda", "id": "50ee543b25a9233d", "uuid": "d19028de-2f78-42bb-bf30-69fe847e1718"}, "__new_primary_file_unique.unique.pasture|0.36.unique.pasture__": {"src": "hda", "id": "c5a46b89f297f5cc", "uuid": "d5d615f3-7ef5-48df-93b5-39dcc2af1e5e"}, "__new_primary_file_unique.unique.pasture|unique.unique.pasture__": {"src": "hda", "id": "7e2564a05bcc37a3", "uuid": "adbcacd7-f625-44e8-aff6-c182a725a54b"}, "__new_primary_file_unique.unique.pasture|0.29.unique.pasture__": {"src": "hda", "id": "eb329b1ce8fe2773", "uuid": "8cf75325-c1aa-4857-b009-74a8f25c8851"}, "__new_primary_file_unique.unique.pasture|0.27.unique.pasture__": {"src": "hda", "id": "011d5380a212a555", "uuid": "dda5a7f8-54ff-48df-af64-3ff6130a0023"}, "__new_primary_file_unique.unique.pasture|0.19.unique.pasture__": {"src": "hda", "id": "a77423a55da368e3", "uuid": "f1239609-5743-4c9f-9243-76c541bdb9bb"}, "__new_primary_file_unique.unique.pasture|0.26.unique.pasture__": {"src": "hda", "id": "6261490a58dd5bd4", "uuid": "baa0b45e-cb4c-4929-ad1c-ffba063ccb02"}, "__new_primary_file_unique.unique.pasture|0.15.unique.pasture__": {"src": "hda", "id": "3fe313b443859214", "uuid": "570ab633-d41d-48d8-9cf7-e771d2c3cc2f"}, "__new_primary_file_unique.unique.pasture|0.04.unique.pasture__": {"src": "hda", "id": "0f4fd06d624bc101", "uuid": "bf126e7c-1646-461b-bc1d-3d83eff9a600"}, "__new_primary_file_unique.unique.pasture|0.08.unique.pasture__": {"src": "hda", "id": "85e8ecefb7a860ea", "uuid": "17fbd0f3-46e0-488b-9961-937fea3cba44"}, "__new_primary_file_unique.unique.pasture|0.24.unique.pasture__": {"src": "hda", "id": "371b51682aba3c7b", "uuid": "302f844f-f79f-4a42-b4e7-890e4d85bd45"}, "__new_primary_file_unique.unique.pasture|0.01.unique.pasture__": {"src": "hda", "id": "efb1b99b3edb7343", "uuid": "f449d3c5-8b9e-45df-971b-0d1e6fd4e853"}, "__new_primary_file_unique.unique.pasture|0.10.unique.pasture__": {"src": "hda", "id": "06eac525c92ec5de", "uuid": "0d13a28c-8c50-4d7f-8ebe-079ef9ec2874"}, "__new_primary_file_unique.unique.pasture|0.11.unique.pasture__": {"src": "hda", "id": "85d8593222a5f623", "uuid": "a2ba2714-ae96-436e-86b7-c67e97c34670"}, "__new_primary_file_unique.unique.pasture|0.21.unique.pasture__": {"src": "hda", "id": "7e35c6c406c695d9", "uuid": "7bcb4870-2a34-4170-98df-b02bcaffa8e3"}, "__new_primary_file_unique.unique.pasture|0.33.unique.pasture__": {"src": "hda", "id": "c3a0cd9a34f8c4f4", "uuid": "1f85a875-70d0-4a38-84b6-ee7cfed4b764"}, "logfile": {"src": "hda", "id": "035475ec449588b1", "uuid": "2240c935-ca06-45ff-838f-8f41eef1319d"}, "__new_primary_file_unique.unique.pasture|0.03.unique.pasture__": {"src": "hda", "id": "f70fd0893b00e2ab", "uuid": "7cb952af-0619-4a0f-afc4-9d1eb18a232c"}, "__new_primary_file_unique.unique.pasture|0.38.unique.pasture__": {"src": "hda", "id": "491bfe2fea6003a3", "uuid": "122cae7c-aa29-4832-8ce7-3c4ebc850373"}, "__new_primary_file_unique.unique.pasture|0.05.unique.pasture__": {"src": "hda", "id": "35f0f6185017fb1f", "uuid": "d0439572-964a-48e3-8d3e-e74ee882c6c2"}, "__new_primary_file_unique.unique.pasture|0.25.unique.pasture__": {"src": "hda", "id": "d9e7f0348948aedc", "uuid": "ff32829c-1011-488f-ad52-8432f3ec5913"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sharedseqs(shared=infile_otu.dat,uniquegroups=pasture)\nunique\t48\n0.01\t46\n0.02\t43\n0.03\t42\n0.04\t39\n0.05\t35\n0.06\t30\n0.07\t28\n0.08\t23\n0.09\t23\n0.10\t22\n0.11\t19\n0.12\t17\n0.13\t16\n0.14\t13\n0.15\t12\n0.16\t11\n0.17\t10\n0.18\t9\n0.19\t8\n0.20\t7\n0.21\t7\n0.22\t6\n0.23\t6\n0.24\t4\n0.25\t3\n0.26\t2\n0.27\t2\n0.29\t2\n0.32\t1\n0.33\t1\n0.36\t1\n0.38\t1\n0.41\t1\n0.45\t0 - No otus shared by groups  pasture.\n0.55\t0 - No otus shared by groups  pasture.\n\nOutput File Names: \ninfile_otu.unique.unique.pasture.shared.seqs\ninfile_otu.0.01.unique.pasture.shared.seqs\ninfile_otu.0.02.unique.pasture.shared.seqs\ninfile_otu.0.03.unique.pasture.shared.seqs\ninfile_otu.0.04.unique.pasture.shared.seqs\ninfile_otu.0.05.unique.pasture.shared.seqs\ninfile_otu.0.06.unique.pasture.shared.seqs\ninfile_otu.0.07.unique.pasture.shared.seqs\ninfile_otu.0.08.unique.pasture.shared.seqs\ninfile_otu.0.09.unique.pasture.shared.seqs\ninfile_otu.0.10.unique.pasture.shared.seqs\ninfile_otu.0.11.unique.pasture.shared.seqs\ninfile_otu.0.12.unique.pasture.shared.seqs\ninfile_otu.0.13.unique.pasture.shared.seqs\ninfile_otu.0.14.unique.pasture.shared.seqs\ninfile_otu.0.15.unique.pasture.shared.seqs\ninfile_otu.0.16.unique.pasture.shared.seqs\ninfile_otu.0.17.unique.pasture.shared.seqs\ninfile_otu.0.18.unique.pasture.shared.seqs\ninfile_otu.0.19.unique.pasture.shared.seqs\ninfile_otu.0.20.unique.pasture.shared.seqs\ninfile_otu.0.21.unique.pasture.shared.seqs\ninfile_otu.0.22.unique.pasture.shared.seqs\ninfile_otu.0.23.unique.pasture.shared.seqs\ninfile_otu.0.24.unique.pasture.shared.seqs\ninfile_otu.0.25.unique.pasture.shared.seqs\ninfile_otu.0.26.unique.pasture.shared.seqs\ninfile_otu.0.27.unique.pasture.shared.seqs\ninfile_otu.0.29.unique.pasture.shared.seqs\ninfile_otu.0.32.unique.pasture.shared.seqs\ninfile_otu.0.33.unique.pasture.shared.seqs\ninfile_otu.0.36.unique.pasture.shared.seqs\ninfile_otu.0.38.unique.pasture.shared.seqs\ninfile_otu.0.41.unique.pasture.shared.seqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1329.dat' infile_otu.dat &&  echo 'get.sharedseqs( shared=infile_otu.dat ,uniquegroups=pasture )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:41:40.469435", "params": {"output": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"seqsfrom\": {\"selection\": \"unique\", \"groups\": \"pasture\", \"__current_case__\": 0}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1329}]}, \"__current_case__\": 0, \"label\": null}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22093", "id": "6cc323ea174af743", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sharedseqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"infile|intype": "in_shared", "infile|otu": {"src": "hda", "id": "b411495052c9266d"}, "output": "accnos"}, "job": {"inputs": {"otu": {"src": "hda", "id": "b411495052c9266d", "uuid": "7c6eb3c4-6f8d-4d18-9537-c10cfa1e409d"}}, "update_time": "2018-02-08T17:42:06.077218", "tool_id": "mothur_get_sharedseqs", "outputs": {"__new_primary_file_0.55.unique.forest_pasture|0.01.unique.forest_pasture__": {"src": "hda", "id": "9d500f70f1832c83", "uuid": "ac9d5a45-2acb-46d5-b1f9-5e003ed19514"}, "__new_primary_file_0.55.unique.forest_pasture|0.03.unique.forest_pasture__": {"src": "hda", "id": "c1f59ad8186b7258", "uuid": "e7996e0e-6d7b-408b-856d-41452e493a71"}, "__new_primary_file_0.55.unique.forest_pasture|0.12.unique.forest_pasture__": {"src": "hda", "id": "38ac28315a9c1e7b", "uuid": "b1741da4-5466-4887-83be-ad3bc92a2f29"}, "__new_primary_file_0.55.unique.forest_pasture|0.08.unique.forest_pasture__": {"src": "hda", "id": "48cc0123b280b7cb", "uuid": "22a4a8fe-eff7-4452-8a4e-230423b1bf66"}, "__new_primary_file_0.55.unique.forest_pasture|0.36.unique.forest_pasture__": {"src": "hda", "id": "c0a3fdb58381b5de", "uuid": "8c5f4133-31e3-4bf6-8fbc-47df79c017e0"}, "__new_primary_file_0.55.unique.forest_pasture|0.33.unique.forest_pasture__": {"src": "hda", "id": "8616db7f86b8b1fb", "uuid": "c4da094f-0bfc-4e51-a648-16d96bad383e"}, "__new_primary_file_0.55.unique.forest_pasture|0.23.unique.forest_pasture__": {"src": "hda", "id": "0426db8ff8502d52", "uuid": "3f614b76-8d01-41d3-8f0f-43d0654f09c1"}, "__new_primary_file_0.55.unique.forest_pasture|0.32.unique.forest_pasture__": {"src": "hda", "id": "df800ebdaa3024a1", "uuid": "1c15724b-6716-4d9a-8181-a56a0a8edf5d"}, "__new_primary_file_0.55.unique.forest_pasture|0.06.unique.forest_pasture__": {"src": "hda", "id": "7c8b5be6333b2d1a", "uuid": "1ef15538-f50f-4ab3-8b25-a8a105d4218e"}, "__new_primary_file_0.55.unique.forest_pasture|0.45.unique.forest_pasture__": {"src": "hda", "id": "ad0acee00d55703d", "uuid": "4dc1095b-f3a7-42bc-8062-13c9429b332f"}, "__new_primary_file_0.55.unique.forest_pasture|0.38.unique.forest_pasture__": {"src": "hda", "id": "e9a3b80d63e9de81", "uuid": "be08a878-a184-4bdf-9a94-36c570cf0c83"}, "__new_primary_file_0.55.unique.forest_pasture|0.04.unique.forest_pasture__": {"src": "hda", "id": "eb160ab98cd3f367", "uuid": "ad491664-70d2-44b4-87b0-a6c8a8a8c3ce"}, "__new_primary_file_0.55.unique.forest_pasture|0.20.unique.forest_pasture__": {"src": "hda", "id": "f41ba0754147b197", "uuid": "7ded26bf-5321-4726-958d-2e47645beb8d"}, "__new_primary_file_0.55.unique.forest_pasture|0.26.unique.forest_pasture__": {"src": "hda", "id": "354372befa8340f4", "uuid": "b4bd2385-535a-47b6-9a64-11a0d1ef2871"}, "__new_primary_file_0.55.unique.forest_pasture|0.15.unique.forest_pasture__": {"src": "hda", "id": "51ebda391f6af4df", "uuid": "74879c3a-0dd0-4396-b425-74c4f3dabde6"}, "__new_primary_file_0.55.unique.forest_pasture|0.02.unique.forest_pasture__": {"src": "hda", "id": "46d062e2f01a1ecb", "uuid": "10358e21-ef57-425f-b57a-558c9887ed3f"}, "__new_primary_file_0.55.unique.forest_pasture|0.10.unique.forest_pasture__": {"src": "hda", "id": "5f8360fb2204373b", "uuid": "5a37fb75-d0bd-46bb-9201-feab6e8dd465"}, "__new_primary_file_0.55.unique.forest_pasture|0.17.unique.forest_pasture__": {"src": "hda", "id": "7e220261cc1c0de1", "uuid": "a9f9bf84-5ffb-4fd0-a213-69fd1ef62f66"}, "__new_primary_file_0.55.unique.forest_pasture|0.29.unique.forest_pasture__": {"src": "hda", "id": "9d600998684d58e9", "uuid": "8383c705-f2ee-4916-b05a-387552913311"}, "__new_primary_file_0.55.unique.forest_pasture|0.09.unique.forest_pasture__": {"src": "hda", "id": "70c41ebe9fe356e1", "uuid": "a0b9b8e4-2ead-4664-ab22-5a26d0e10b87"}, "__new_primary_file_0.55.unique.forest_pasture|0.22.unique.forest_pasture__": {"src": "hda", "id": "32d143676e069a01", "uuid": "4f54818c-c01b-425d-b9b1-c35bfb348cba"}, "__new_primary_file_0.55.unique.forest_pasture|0.16.unique.forest_pasture__": {"src": "hda", "id": "93f6fc8df710787a", "uuid": "3387ece6-c5f5-4515-9ec5-a9af2c72187f"}, "__new_primary_file_0.55.unique.forest_pasture|0.14.unique.forest_pasture__": {"src": "hda", "id": "0cc0680429283dfc", "uuid": "5efa1f57-520b-4118-9352-c5d7eb89081c"}, "__new_primary_file_0.55.unique.forest_pasture|0.05.unique.forest_pasture__": {"src": "hda", "id": "a57ebb089e76dd90", "uuid": "f9c6e61e-1668-4453-965e-bc29da5bd541"}, "__new_primary_file_0.55.unique.forest_pasture|0.19.unique.forest_pasture__": {"src": "hda", "id": "b0b67d4068ae0475", "uuid": "37dca42d-d112-48a6-b47e-fd2935922124"}, "__new_primary_file_0.55.unique.forest_pasture|0.27.unique.forest_pasture__": {"src": "hda", "id": "1071ff2ef49f04a3", "uuid": "c22998ee-cf2d-40cd-aa75-e5eb706b811f"}, "__new_primary_file_0.55.unique.forest_pasture|0.25.unique.forest_pasture__": {"src": "hda", "id": "8c1fbe4c8d09a4f1", "uuid": "591cca04-40ce-440c-871c-a56201b4b2fe"}, "__new_primary_file_0.55.unique.forest_pasture|0.21.unique.forest_pasture__": {"src": "hda", "id": "bb747ea2094b72f9", "uuid": "ccee3ad4-dade-45eb-b50c-f1e52a66a5ba"}, "__new_primary_file_0.55.unique.forest_pasture|0.11.unique.forest_pasture__": {"src": "hda", "id": "96ad708bb449c3ab", "uuid": "14d7a1e1-dff2-4cc7-b6de-e126d0799ba7"}, "__new_primary_file_0.55.unique.forest_pasture|0.41.unique.forest_pasture__": {"src": "hda", "id": "26447d823670d91d", "uuid": "fafdd585-9a02-47f0-b77d-924961aa608f"}, "__new_primary_file_0.55.unique.forest_pasture|0.13.unique.forest_pasture__": {"src": "hda", "id": "e4017c53abb4d64e", "uuid": "3b1bb461-c82b-48b9-8244-6dbb7e580786"}, "__new_primary_file_0.55.unique.forest_pasture|0.55.unique.forest_pasture__": {"src": "hda", "id": "461a1be07c3de467", "uuid": "4205bfbb-e0f6-4c3d-a99b-010ad75aa6a7"}, "logfile": {"src": "hda", "id": "c800ba3fbc6b74ec", "uuid": "be48e703-21fe-4856-ab8f-8ca6a45c7695"}, "__new_primary_file_0.55.unique.forest_pasture|0.24.unique.forest_pasture__": {"src": "hda", "id": "d65b4a99cdfc8e57", "uuid": "60d7e552-e4e2-414d-8bc3-1a6c30e518c9"}, "__new_primary_file_0.55.unique.forest_pasture|0.07.unique.forest_pasture__": {"src": "hda", "id": "fe0fc1f57508fe50", "uuid": "9b88c871-293e-4e8f-a1e7-1487e70e943e"}, "__new_primary_file_0.55.unique.forest_pasture|0.18.unique.forest_pasture__": {"src": "hda", "id": "f74cebaa6e844ba8", "uuid": "48485671-082f-47e6-bff4-267b328a813c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sharedseqs(shared=infile_otu.dat,output=accnos)\nunique\t0 - No otus shared by groups  forest  pasture.\n0.01\t1\n0.02\t1\n0.03\t2\n0.04\t4\n0.05\t7\n0.06\t9\n0.07\t9\n0.08\t9\n0.09\t9\n0.10\t8\n0.11\t8\n0.12\t8\n0.13\t8\n0.14\t9\n0.15\t9\n0.16\t9\n0.17\t10\n0.18\t10\n0.19\t11\n0.20\t10\n0.21\t9\n0.22\t9\n0.23\t8\n0.24\t7\n0.25\t7\n0.26\t7\n0.27\t6\n0.29\t4\n0.32\t3\n0.33\t2\n0.36\t2\n0.38\t2\n0.41\t1\n0.45\t1\n0.55\t1\n\nOutput File Names: \ninfile_otu.0.01.unique.forest_pasture.accnos\ninfile_otu.0.02.unique.forest_pasture.accnos\ninfile_otu.0.03.unique.forest_pasture.accnos\ninfile_otu.0.04.unique.forest_pasture.accnos\ninfile_otu.0.05.unique.forest_pasture.accnos\ninfile_otu.0.06.unique.forest_pasture.accnos\ninfile_otu.0.07.unique.forest_pasture.accnos\ninfile_otu.0.08.unique.forest_pasture.accnos\ninfile_otu.0.09.unique.forest_pasture.accnos\ninfile_otu.0.10.unique.forest_pasture.accnos\ninfile_otu.0.11.unique.forest_pasture.accnos\ninfile_otu.0.12.unique.forest_pasture.accnos\ninfile_otu.0.13.unique.forest_pasture.accnos\ninfile_otu.0.14.unique.forest_pasture.accnos\ninfile_otu.0.15.unique.forest_pasture.accnos\ninfile_otu.0.16.unique.forest_pasture.accnos\ninfile_otu.0.17.unique.forest_pasture.accnos\ninfile_otu.0.18.unique.forest_pasture.accnos\ninfile_otu.0.19.unique.forest_pasture.accnos\ninfile_otu.0.20.unique.forest_pasture.accnos\ninfile_otu.0.21.unique.forest_pasture.accnos\ninfile_otu.0.22.unique.forest_pasture.accnos\ninfile_otu.0.23.unique.forest_pasture.accnos\ninfile_otu.0.24.unique.forest_pasture.accnos\ninfile_otu.0.25.unique.forest_pasture.accnos\ninfile_otu.0.26.unique.forest_pasture.accnos\ninfile_otu.0.27.unique.forest_pasture.accnos\ninfile_otu.0.29.unique.forest_pasture.accnos\ninfile_otu.0.32.unique.forest_pasture.accnos\ninfile_otu.0.33.unique.forest_pasture.accnos\ninfile_otu.0.36.unique.forest_pasture.accnos\ninfile_otu.0.38.unique.forest_pasture.accnos\ninfile_otu.0.41.unique.forest_pasture.accnos\ninfile_otu.0.45.unique.forest_pasture.accnos\ninfile_otu.0.55.unique.forest_pasture.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1365.dat' infile_otu.dat &&  echo 'get.sharedseqs( shared=infile_otu.dat ,output=accnos )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:42:01.270327", "params": {"output": "\"accnos\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"seqsfrom\": {\"selection\": \"all\", \"__current_case__\": 2}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1365}]}, \"__current_case__\": 0, \"label\": null}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22238", "id": "af2b33d2c4a65f6c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sharedseqs.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"infile|intype": "in_listgroup", "infile|otu": {"src": "hda", "id": "8d91fc817c607b8e"}, "infile|fasta": {"src": "hda", "id": "a6f3a03f0bffe083"}, "infile|group": {"src": "hda", "id": "52f04961369d0fd2"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "a6f3a03f0bffe083", "uuid": "2d9a27af-6077-4f21-9097-f6a9501d960c"}, "group": {"src": "hda", "id": "52f04961369d0fd2", "uuid": "fb77b6ff-8d4f-482a-87b1-bd2181197a17"}, "otu": {"src": "hda", "id": "8d91fc817c607b8e", "uuid": "76253355-c762-48e0-a725-f01d3acd4785"}}, "update_time": "2018-02-08T17:42:37.685956", "tool_id": "mothur_get_sharedseqs", "outputs": {"__new_primary_file_0.55.unique.forest_pasture|0.01.unique.forest_pasture__": {"src": "hda", "id": "511e5219be7d6707", "uuid": "b75edb7a-a1a7-46fa-8bd9-5b6c7f94ad1f"}, "__new_primary_file_0.55.unique.forest_pasture|0.03.unique.forest_pasture__": {"src": "hda", "id": "495f4784edb27bdf", "uuid": "0c2d0402-2f9a-43f9-ba87-40b8214ae564"}, "__new_primary_file_0.55.unique.forest_pasture|0.12.unique.forest_pasture__": {"src": "hda", "id": "9591777882159fea", "uuid": "028d0537-b9ab-4a69-93fc-0c8c44a0b8bf"}, "__new_primary_file_0.55.unique.forest_pasture|0.08.unique.forest_pasture__": {"src": "hda", "id": "6a717f18c0f373ef", "uuid": "16d90ea0-5922-4de6-a4d0-c81d4db1ad43"}, "__new_primary_file_0.55.unique.forest_pasture|0.36.unique.forest_pasture__": {"src": "hda", "id": "b4da54e0b157a0e8", "uuid": "a3762dc8-b855-4b87-bdac-ea10ce2b12cd"}, "__new_primary_file_0.55.unique.forest_pasture|0.33.unique.forest_pasture__": {"src": "hda", "id": "dbe0036ded1c1b07", "uuid": "79bbcc76-86f5-4afd-9e61-57fc3a8fb811"}, "__new_primary_file_0.55.unique.forest_pasture|0.23.unique.forest_pasture__": {"src": "hda", "id": "f6c1555750ef1ba5", "uuid": "19f1c7c2-ec2f-46c7-93da-845760389a1f"}, "__new_primary_file_0.55.unique.forest_pasture|0.32.unique.forest_pasture__": {"src": "hda", "id": "8701122ca649ef0e", "uuid": "fa3abfc6-e430-459f-b80b-45f289b43b73"}, "__new_primary_file_0.55.unique.forest_pasture|0.06.unique.forest_pasture__": {"src": "hda", "id": "c1456ecfdc824977", "uuid": "16b1c6bc-df83-4831-acf1-bab966123e0c"}, "__new_primary_file_0.55.unique.forest_pasture|0.45.unique.forest_pasture__": {"src": "hda", "id": "00a57718e499b089", "uuid": "34e53b49-a4f9-4760-8212-a8a75c95d923"}, "__new_primary_file_0.55.unique.forest_pasture|0.38.unique.forest_pasture__": {"src": "hda", "id": "bbd0b9f57a884d99", "uuid": "447bac35-36b3-4950-aa8a-92281792870d"}, "__new_primary_file_0.55.unique.forest_pasture|0.04.unique.forest_pasture__": {"src": "hda", "id": "db9feb02278bde1e", "uuid": "eff3a8da-9526-4a5c-9006-a4534adc087f"}, "__new_primary_file_0.55.unique.forest_pasture|0.20.unique.forest_pasture__": {"src": "hda", "id": "a0b6b71fdb91e8d6", "uuid": "07d2fd80-4a5a-4b71-a109-418ada75f9b0"}, "__new_primary_file_0.55.unique.forest_pasture|0.26.unique.forest_pasture__": {"src": "hda", "id": "fdc43dbaf89861e9", "uuid": "d9913622-9724-4e7a-a258-71e4b51d7e74"}, "__new_primary_file_0.55.unique.forest_pasture|0.15.unique.forest_pasture__": {"src": "hda", "id": "818a1a9068d181a2", "uuid": "0e930c59-88a7-4170-9b62-baeb973ba3d2"}, "__new_primary_file_0.55.unique.forest_pasture|0.02.unique.forest_pasture__": {"src": "hda", "id": "c192547d733b6f1c", "uuid": "1e0d0127-6b96-4f83-b731-a68c42755eb2"}, "__new_primary_file_0.55.unique.forest_pasture|0.10.unique.forest_pasture__": {"src": "hda", "id": "68ce0d2a7fd661e7", "uuid": "3a586980-5f0e-4267-afcb-cdb1ff68ac90"}, "__new_primary_file_0.55.unique.forest_pasture|0.17.unique.forest_pasture__": {"src": "hda", "id": "a4f459b907c399cc", "uuid": "81125254-4e5c-4a19-b1d9-ac782b94a317"}, "__new_primary_file_0.55.unique.forest_pasture|0.29.unique.forest_pasture__": {"src": "hda", "id": "19ae04e79b51d442", "uuid": "8bf52cda-02f4-4749-b29f-a3487c96dc6b"}, "__new_primary_file_0.55.unique.forest_pasture|0.09.unique.forest_pasture__": {"src": "hda", "id": "5d27d481e44c798e", "uuid": "3f7e8f14-2bf7-4ecc-92bb-38830620303a"}, "__new_primary_file_0.55.unique.forest_pasture|0.22.unique.forest_pasture__": {"src": "hda", "id": "dea178949647e385", "uuid": "c2bb8d24-ef0e-4f4d-b41c-9ec355fb161c"}, "__new_primary_file_0.55.unique.forest_pasture|0.16.unique.forest_pasture__": {"src": "hda", "id": "60abf49d2417a732", "uuid": "5ab2df46-7bf9-48cd-9f2a-8235c07b4ece"}, "__new_primary_file_0.55.unique.forest_pasture|0.14.unique.forest_pasture__": {"src": "hda", "id": "df7b712664e24f20", "uuid": "57cdb709-5dc3-4c57-9f22-724485952ec1"}, "__new_primary_file_0.55.unique.forest_pasture|0.05.unique.forest_pasture__": {"src": "hda", "id": "d4dc7f05ea35c530", "uuid": "511277c8-c696-4c57-9596-32ff3df816a5"}, "__new_primary_file_0.55.unique.forest_pasture|0.19.unique.forest_pasture__": {"src": "hda", "id": "600dc09e02076335", "uuid": "0d6d7fc0-6d50-40ff-a8e1-0a416fe81103"}, "__new_primary_file_0.55.unique.forest_pasture|0.27.unique.forest_pasture__": {"src": "hda", "id": "eec4effe5fe2e4fa", "uuid": "cc5bf893-19a5-4af9-a3b1-4d5be8a84477"}, "__new_primary_file_0.55.unique.forest_pasture|0.25.unique.forest_pasture__": {"src": "hda", "id": "694ae81ce1930e68", "uuid": "b5e2809c-a837-4e87-b2f7-0a3f5068ac37"}, "__new_primary_file_0.55.unique.forest_pasture|0.21.unique.forest_pasture__": {"src": "hda", "id": "7106c2d6deef3cfa", "uuid": "c3816365-54f1-46f7-b523-60785a851f05"}, "__new_primary_file_0.55.unique.forest_pasture|0.11.unique.forest_pasture__": {"src": "hda", "id": "37d3583ea310e337", "uuid": "2df63967-e61b-4b07-bb20-49fa9aa30f17"}, "__new_primary_file_0.55.unique.forest_pasture|0.41.unique.forest_pasture__": {"src": "hda", "id": "eafabd3a383ab29e", "uuid": "63045926-44cb-495f-b9fb-f5a3e2851045"}, "__new_primary_file_0.55.unique.forest_pasture|0.13.unique.forest_pasture__": {"src": "hda", "id": "48b1ebf5a933ed38", "uuid": "90e6083a-29ca-49e2-b0c2-b0df7d244195"}, "__new_primary_file_0.55.unique.forest_pasture|0.55.unique.forest_pasture__": {"src": "hda", "id": "cca6a764eaebccae", "uuid": "c04f97c4-be79-4d23-8380-e93ffe77f2a1"}, "logfile": {"src": "hda", "id": "739c965d51d75f3b", "uuid": "7863b87c-b2fe-429e-920d-4a3da20c400b"}, "__new_primary_file_0.55.unique.forest_pasture|0.24.unique.forest_pasture__": {"src": "hda", "id": "d759666b93a781e8", "uuid": "1ac20ea6-2a85-40e0-a743-1046218a57e4"}, "__new_primary_file_0.55.unique.forest_pasture|0.07.unique.forest_pasture__": {"src": "hda", "id": "e6e0520fd65a4854", "uuid": "d18d49ee-df35-44b8-be0e-d19c51c750e8"}, "__new_primary_file_0.55.unique.forest_pasture|0.18.unique.forest_pasture__": {"src": "hda", "id": "e3d16ba9dbc1647b", "uuid": "6f753123-ea6c-4c27-8326-f26036a39360"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > get.sharedseqs(list=infile_otu.dat,group=infile.group.dat,fasta=infile_ \rfasta.dat)\nunique\t0 - No otus shared by groups  forest  pasture.\n0.01\t1\n0.02\t1\n0.03\t2\n0.04\t4\n0.05\t7\n0.06\t9\n0.07\t9\n0.08\t9\n0.09\t9\n0.10\t8\n0.11\t8\n0.12\t8\n0.13\t8\n0.14\t9\n0.15\t9\n0.16\t9\n0.17\t10\n0.18\t10\n0.19\t11\n0.20\t10\n0.21\t9\n0.22\t9\n0.23\t8\n0.24\t7\n0.25\t7\n0.26\t7\n0.27\t6\n0.29\t4\n0.32\t3\n0.33\t2\n0.36\t2\n0.38\t2\n0.41\t1\n0.45\t1\n0.55\t1\n\nOutput File Names: \ninfile_otu.0.01.unique.forest_pasture.shared.seqs\ninfile_fasta.0.01.unique.forest_pasture.shared.fasta\ninfile_otu.0.02.unique.forest_pasture.shared.seqs\ninfile_fasta.0.02.unique.forest_pasture.shared.fasta\ninfile_otu.0.03.unique.forest_pasture.shared.seqs\ninfile_fasta.0.03.unique.forest_pasture.shared.fasta\ninfile_otu.0.04.unique.forest_pasture.shared.seqs\ninfile_fasta.0.04.unique.forest_pasture.shared.fasta\ninfile_otu.0.05.unique.forest_pasture.shared.seqs\ninfile_fasta.0.05.unique.forest_pasture.shared.fasta\ninfile_otu.0.06.unique.forest_pasture.shared.seqs\ninfile_fasta.0.06.unique.forest_pasture.shared.fasta\ninfile_otu.0.07.unique.forest_pasture.shared.seqs\ninfile_fasta.0.07.unique.forest_pasture.shared.fasta\ninfile_otu.0.08.unique.forest_pasture.shared.seqs\ninfile_fasta.0.08.unique.forest_pasture.shared.fasta\ninfile_otu.0.09.unique.forest_pasture.shared.seqs\ninfile_fasta.0.09.unique.forest_pasture.shared.fasta\ninfile_otu.0.10.unique.forest_pasture.shared.seqs\ninfile_fasta.0.10.unique.forest_pasture.shared.fasta\ninfile_otu.0.11.unique.forest_pasture.shared.seqs\ninfile_fasta.0.11.unique.forest_pasture.shared.fasta\ninfile_otu.0.12.unique.forest_pasture.shared.seqs\ninfile_fasta.0.12.unique.forest_pasture.shared.fasta\ninfile_otu.0.13.unique.forest_pasture.shared.seqs\ninfile_fasta.0.13.unique.forest_pasture.shared.fasta\ninfile_otu.0.14.unique.forest_pasture.shared.seqs\ninfile_fasta.0.14.unique.forest_pasture.shared.fasta\ninfile_otu.0.15.unique.forest_pasture.shared.seqs\ninfile_fasta.0.15.unique.forest_pasture.shared.fasta\ninfile_otu.0.16.unique.forest_pasture.shared.seqs\ninfile_fasta.0.16.unique.forest_pasture.shared.fasta\ninfile_otu.0.17.unique.forest_pasture.shared.seqs\ninfile_fasta.0.17.unique.forest_pasture.shared.fasta\ninfile_otu.0.18.unique.forest_pasture.shared.seqs\ninfile_fasta.0.18.unique.forest_pasture.shared.fasta\ninfile_otu.0.19.unique.forest_pasture.shared.seqs\ninfile_fasta.0.19.unique.forest_pasture.shared.fasta\ninfile_otu.0.20.unique.forest_pasture.shared.seqs\ninfile_fasta.0.20.unique.forest_pasture.shared.fasta\ninfile_otu.0.21.unique.forest_pasture.shared.seqs\ninfile_fasta.0.21.unique.forest_pasture.shared.fasta\ninfile_otu.0.22.unique.forest_pasture.shared.seqs\ninfile_fasta.0.22.unique.forest_pasture.shared.fasta\ninfile_otu.0.23.unique.forest_pasture.shared.seqs\ninfile_fasta.0.23.unique.forest_pasture.shared.fasta\ninfile_otu.0.24.unique.forest_pasture.shared.seqs\ninfile_fasta.0.24.unique.forest_pasture.shared.fasta\ninfile_otu.0.25.unique.forest_pasture.shared.seqs\ninfile_fasta.0.25.unique.forest_pasture.shared.fasta\ninfile_otu.0.26.unique.forest_pasture.shared.seqs\ninfile_fasta.0.26.unique.forest_pasture.shared.fasta\ninfile_otu.0.27.unique.forest_pasture.shared.seqs\ninfile_fasta.0.27.unique.forest_pasture.shared.fasta\ninfile_otu.0.29.unique.forest_pasture.shared.seqs\ninfile_fasta.0.29.unique.forest_pasture.shared.fasta\ninfile_otu.0.32.unique.forest_pasture.shared.seqs\ninfile_fasta.0.32.unique.forest_pasture.shared.fasta\ninfile_otu.0.33.unique.forest_pasture.shared.seqs\ninfile_fasta.0.33.unique.forest_pasture.shared.fasta\ninfile_otu.0.36.unique.forest_pasture.shared.seqs\ninfile_fasta.0.36.unique.forest_pasture.shared.fasta\ninfile_otu.0.38.unique.forest_pasture.shared.seqs\ninfile_fasta.0.38.unique.forest_pasture.shared.fasta\ninfile_otu.0.41.unique.forest_pasture.shared.seqs\ninfile_fasta.0.41.unique.forest_pasture.shared.fasta\ninfile_otu.0.45.unique.forest_pasture.shared.seqs\ninfile_fasta.0.45.unique.forest_pasture.shared.fasta\ninfile_otu.0.55.unique.forest_pasture.shared.seqs\ninfile_fasta.0.55.unique.forest_pasture.shared.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1402.dat' infile_otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1403.dat' infile.group.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1404.dat' infile_fasta.dat && ln -s 'None' count_in.dat &&  echo 'get.sharedseqs( list=infile_otu.dat  ,group=infile.group.dat  ,fasta=infile_fasta.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:42:29.966838", "params": {"output": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"group\": {\"values\": [{\"src\": \"hda\", \"id\": 1403}]}, \"intype\": \"in_listgroup\", \"seqsfrom\": {\"selection\": \"all\", \"__current_case__\": 2}, \"count_in\": null, \"label\": null, \"__current_case__\": 1, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 1404}]}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1402}]}}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22500", "id": "721a73f13e9921b7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_get_sharedseqs.test_tool_000005", "has_data": true}, {"data": {"status": "success", "inputs": {"input|has_groups": "no", "input|otu": {"src": "hda", "id": "5aa4434a5de39ae3"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "5aa4434a5de39ae3", "uuid": "3fad1be5-92c7-499a-ad97-4df17029bb79"}}, "update_time": "2018-02-08T17:43:07.439864", "tool_id": "mothur_heatmap_bin", "outputs": {"__new_primary_file_unique.heatmap|0.12.heatmap__": {"src": "hda", "id": "3736958d98c85038", "uuid": "a4133262-f568-437b-ae4f-0da9fcdc8592"}, "__new_primary_file_unique.heatmap|0.16.heatmap__": {"src": "hda", "id": "1d7e16e67c25e161", "uuid": "fdd59c4f-5407-4ed2-8d14-3e1fac5c483a"}, "__new_primary_file_unique.heatmap|0.19.heatmap__": {"src": "hda", "id": "8d3b08d9b3af5f9c", "uuid": "0936eae7-66f4-4c4d-9b32-6a9ecc1ceb1b"}, "__new_primary_file_unique.heatmap|0.17.heatmap__": {"src": "hda", "id": "470eb1f9703ec6ce", "uuid": "ed2b8799-1815-42b9-996e-a99acc109c9a"}, "__new_primary_file_unique.heatmap|0.15.heatmap__": {"src": "hda", "id": "f122c84b34480f3c", "uuid": "5b37b1a5-8639-4277-a8d7-e41cef4802b5"}, "__new_primary_file_unique.heatmap|0.04.heatmap__": {"src": "hda", "id": "191aad2a235a14a2", "uuid": "1955e26c-38f5-4edb-9875-4bf51ee8342c"}, "__new_primary_file_unique.heatmap|0.38.heatmap__": {"src": "hda", "id": "628d782395597178", "uuid": "cfa9705a-42a7-49f9-a6b8-eeda2fbf9a7d"}, "__new_primary_file_unique.heatmap|0.08.heatmap__": {"src": "hda", "id": "366694fb7dd8b44f", "uuid": "b38393d5-0012-44bf-87e5-0aa6e0ebe15d"}, "__new_primary_file_unique.heatmap|unique.heatmap__": {"src": "hda", "id": "8c18965d948ad2eb", "uuid": "60e0ce24-ffa5-4839-a210-6b1bf86df3f0"}, "__new_primary_file_unique.heatmap|0.03.heatmap__": {"src": "hda", "id": "df6c40d10f33a9c4", "uuid": "2479c797-9034-4618-aa53-3c362bfb967b"}, "__new_primary_file_unique.heatmap|0.05.heatmap__": {"src": "hda", "id": "fa1197388b314251", "uuid": "d249805c-a8b5-4ad7-94e5-6a31ed6955d9"}, "__new_primary_file_unique.heatmap|0.33.heatmap__": {"src": "hda", "id": "567a86d1273a635a", "uuid": "49e3f568-909e-4cde-843e-76d6e45160eb"}, "__new_primary_file_unique.heatmap|0.55.heatmap__": {"src": "hda", "id": "3dcdd65bc248798d", "uuid": "aa8e807a-e12a-4d81-ad9b-44d357fdf341"}, "__new_primary_file_unique.heatmap|0.25.heatmap__": {"src": "hda", "id": "80a31c7cff5bc197", "uuid": "6a95e2a7-00ad-4cca-85fa-7b81c163a913"}, "__new_primary_file_unique.heatmap|0.18.heatmap__": {"src": "hda", "id": "e2e89d7da5281839", "uuid": "d1514716-4259-4a64-b1dd-5c25fafd4840"}, "__new_primary_file_unique.heatmap|0.09.heatmap__": {"src": "hda", "id": "2daeae546a05fdec", "uuid": "062f23d1-8d05-42f6-80b3-814a5becc446"}, "__new_primary_file_unique.heatmap|0.22.heatmap__": {"src": "hda", "id": "b9010d0fbfd5e1f7", "uuid": "0eb1d487-49d3-4765-aede-99028c87eb25"}, "__new_primary_file_unique.heatmap|0.45.heatmap__": {"src": "hda", "id": "0ff6ef528fac88f3", "uuid": "19750f5c-20b0-4b56-8c88-233ed11b9cb0"}, "__new_primary_file_unique.heatmap|0.29.heatmap__": {"src": "hda", "id": "8b81c0162ce5557e", "uuid": "05a40fec-e894-49da-9985-93ef305650dd"}, "__new_primary_file_unique.heatmap|0.06.heatmap__": {"src": "hda", "id": "349e07445c4e628f", "uuid": "de68102a-f9cc-444d-91a9-01493c828eb8"}, "__new_primary_file_unique.heatmap|0.23.heatmap__": {"src": "hda", "id": "bdd6007a61f34fac", "uuid": "7596babd-1026-4a65-ba1a-686ee58ee90c"}, "__new_primary_file_unique.heatmap|0.01.heatmap__": {"src": "hda", "id": "43f1006025db5fee", "uuid": "e30e539b-e9a3-4679-b312-b8a7d9cbf0ac"}, "__new_primary_file_unique.heatmap|0.20.heatmap__": {"src": "hda", "id": "b47c5be399df737a", "uuid": "889338cc-898b-4c1b-9b56-7f4b8e8dfe4c"}, "__new_primary_file_unique.heatmap|0.41.heatmap__": {"src": "hda", "id": "fdeb460c0475206a", "uuid": "0175d58e-1ff2-4bc5-bd9a-43ffde415d18"}, "__new_primary_file_unique.heatmap|0.02.heatmap__": {"src": "hda", "id": "dd82c12810a978c9", "uuid": "0162abb7-41c1-4785-9bf5-a460d3c66373"}, "__new_primary_file_unique.heatmap|0.13.heatmap__": {"src": "hda", "id": "012f7b1e3f7879e3", "uuid": "16ce423b-1008-4ec2-91ac-f045cb5a5abd"}, "__new_primary_file_unique.heatmap|0.24.heatmap__": {"src": "hda", "id": "51e1e30118f27d1d", "uuid": "aa7d5d3a-c8e7-4637-9506-f5dc4713625d"}, "__new_primary_file_unique.heatmap|0.26.heatmap__": {"src": "hda", "id": "46d5d629e90b7c88", "uuid": "c4d18a20-3db4-4990-b571-659cb5f67d2b"}, "__new_primary_file_unique.heatmap|0.07.heatmap__": {"src": "hda", "id": "91a333426dbcec14", "uuid": "db8c22f8-2c63-45f5-bcf5-e8666607e632"}, "logfile": {"src": "hda", "id": "ef02fd8e80dbdfd0", "uuid": "aa179a93-b92f-4b4b-9123-4e1e6ab34654"}, "__new_primary_file_unique.heatmap|0.36.heatmap__": {"src": "hda", "id": "54e503415a2c0682", "uuid": "d217e5c4-2c11-4de9-ac5e-3cf61b04e274"}, "__new_primary_file_unique.heatmap|0.21.heatmap__": {"src": "hda", "id": "4900c210ae216634", "uuid": "84df347a-bca2-47af-8a5c-8dda81faf549"}, "__new_primary_file_unique.heatmap|0.27.heatmap__": {"src": "hda", "id": "896ea37ce7a39150", "uuid": "53367c7d-546e-4f64-b0d8-d45f2cea1880"}, "__new_primary_file_unique.heatmap|0.32.heatmap__": {"src": "hda", "id": "cf000b2b198e45cc", "uuid": "f69d2d62-be86-42bf-9de8-5485a3fa524d"}, "__new_primary_file_unique.heatmap|0.10.heatmap__": {"src": "hda", "id": "4ab6b94dd0ff726f", "uuid": "b5e27a95-bea7-4c09-972c-0df95a595e53"}, "__new_primary_file_unique.heatmap|0.11.heatmap__": {"src": "hda", "id": "c2eb533b1a115fca", "uuid": "09275784-5714-4597-9aac-4a47deffee64"}, "__new_primary_file_unique.heatmap|0.14.heatmap__": {"src": "hda", "id": "f991b410e4f25497", "uuid": "6cf90f48-02ed-4ec4-aa8f-2ecb520549c0"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > heatmap.bin(list=input_otu.dat,scale=log10,sorted=shared,numotu=0,fonts \rize=24)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.unique.heatmap.bin.svg\ninput_otu.0.01.heatmap.bin.svg\ninput_otu.0.02.heatmap.bin.svg\ninput_otu.0.03.heatmap.bin.svg\ninput_otu.0.04.heatmap.bin.svg\ninput_otu.0.05.heatmap.bin.svg\ninput_otu.0.06.heatmap.bin.svg\ninput_otu.0.07.heatmap.bin.svg\ninput_otu.0.08.heatmap.bin.svg\ninput_otu.0.09.heatmap.bin.svg\ninput_otu.0.10.heatmap.bin.svg\ninput_otu.0.11.heatmap.bin.svg\ninput_otu.0.12.heatmap.bin.svg\ninput_otu.0.13.heatmap.bin.svg\ninput_otu.0.14.heatmap.bin.svg\ninput_otu.0.15.heatmap.bin.svg\ninput_otu.0.16.heatmap.bin.svg\ninput_otu.0.17.heatmap.bin.svg\ninput_otu.0.18.heatmap.bin.svg\ninput_otu.0.19.heatmap.bin.svg\ninput_otu.0.20.heatmap.bin.svg\ninput_otu.0.21.heatmap.bin.svg\ninput_otu.0.22.heatmap.bin.svg\ninput_otu.0.23.heatmap.bin.svg\ninput_otu.0.24.heatmap.bin.svg\ninput_otu.0.25.heatmap.bin.svg\ninput_otu.0.26.heatmap.bin.svg\ninput_otu.0.27.heatmap.bin.svg\ninput_otu.0.29.heatmap.bin.svg\ninput_otu.0.32.heatmap.bin.svg\ninput_otu.0.33.heatmap.bin.svg\ninput_otu.0.36.heatmap.bin.svg\ninput_otu.0.38.heatmap.bin.svg\ninput_otu.0.41.heatmap.bin.svg\ninput_otu.0.45.heatmap.bin.svg\ninput_otu.0.55.heatmap.bin.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1476.dat' input_otu.dat &&  echo 'heatmap.bin( list=input_otu.dat, scale=log10, sorted=shared, numotu=0, fontsize=24 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:43:02.760839", "params": {"scale": "\"log10\"", "numotu": "\"0\"", "dbkey": "\"hg17\"", "fontsize": "\"24\"", "input": "{\"label\": null, \"has_groups\": \"no\", \"__current_case__\": 0, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1476}]}}", "sorted": "\"shared\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22663", "id": "943b175492f370d8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_heatmap_bin.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input|label": "0.26", "input|has_groups": "yes", "input|groups": "forest", "input|otu": {"src": "hda", "id": "1d330b92b21a7ce0"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "1d330b92b21a7ce0", "uuid": "69cae532-4ced-4046-9a3b-44ccc865523d"}}, "update_time": "2018-02-08T17:43:21.076293", "tool_id": "mothur_heatmap_bin", "outputs": {"__new_primary_file_0.26.heatmap|0.26.heatmap__": {"src": "hda", "id": "f381faf65e5272fe", "uuid": "52ee9e76-a05d-4262-a98c-53120394753d"}, "logfile": {"src": "hda", "id": "f2f802538148d8ec", "uuid": "cafa5f29-4a43-4d35-8911-c2515cd598bc"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > heatmap.bin(relabund=input_otu.dat,groups=forest,label=0.26,scale=log10 \r,sorted=shared,numotu=0,fontsize=24)\n0.26\n\nOutput File Names: \ninput_otu.0.26.heatmap.bin.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1514.dat' input_otu.dat &&  echo 'heatmap.bin( relabund=input_otu.dat, groups=forest, label=0.26, scale=log10, sorted=shared, numotu=0, fontsize=24 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:43:17.969781", "params": {"scale": "\"log10\"", "numotu": "\"0\"", "dbkey": "\"hg17\"", "fontsize": "\"24\"", "input": "{\"groups\": \"forest\", \"label\": \"0.26\", \"has_groups\": \"yes\", \"__current_case__\": 1, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1514}]}}", "sorted": "\"shared\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22755", "id": "4b36d8f744e89cdc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_heatmap_bin.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"scale": "linear", "input|groups": ["forest", "pasture"], "input|label": ["0.03", "0.26", "0.55"], "input|otu": {"src": "hda", "id": "838bdf0d25da8928"}, "fontsize": "100", "input|has_groups": "yes", "sorted": "none"}, "job": {"inputs": {"otu": {"src": "hda", "id": "838bdf0d25da8928", "uuid": "a08df5d6-0bf7-453b-9dcd-797fff213c07"}}, "update_time": "2018-02-08T17:43:33.535279", "tool_id": "mothur_heatmap_bin", "outputs": {"__new_primary_file_0.55.heatmap|0.03.heatmap__": {"src": "hda", "id": "b56e6f3aa0b63b69", "uuid": "cc96fe1f-0c4d-4359-8aea-36af82e05f9d"}, "__new_primary_file_0.55.heatmap|0.55.heatmap__": {"src": "hda", "id": "b3785c43e2c86bb3", "uuid": "0f68e509-eec7-4eb9-94b3-8ba0fca3f4be"}, "logfile": {"src": "hda", "id": "662c759ed032ed85", "uuid": "75d94a1d-5eb2-4ac0-8a8b-9c392002d639"}, "__new_primary_file_0.55.heatmap|0.26.heatmap__": {"src": "hda", "id": "50241e2b025a0fb6", "uuid": "cc33ffac-52bc-4567-a598-9fe45db09331"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > heatmap.bin(shared=input_otu.dat,groups=forest-pasture,label=0.03-0.26- \r0.55,scale=linear,sorted=none,numotu=0,fontsize=100)\n0.03\n0.26\n0.55\n\nOutput File Names: \ninput_otu.0.03.heatmap.bin.svg\ninput_otu.0.26.heatmap.bin.svg\ninput_otu.0.55.heatmap.bin.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1517.dat' input_otu.dat &&  echo 'heatmap.bin( shared=input_otu.dat, groups=forest-pasture, label=0.03-0.26-0.55, scale=linear, sorted=none, numotu=0, fontsize=100 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:43:30.569021", "params": {"scale": "\"linear\"", "numotu": "\"0\"", "dbkey": "\"hg17\"", "fontsize": "\"100\"", "input": "{\"groups\": [\"forest\", \"pasture\"], \"label\": [\"0.03\", \"0.26\", \"0.55\"], \"has_groups\": \"yes\", \"__current_case__\": 1, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1517}]}}", "sorted": "\"none\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22841", "id": "07fd1c8ec8f13176", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_heatmap_bin.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input|dist": {"src": "hda", "id": "5580169e77bda3db"}, "input|source": "phylip"}, "job": {"inputs": {"dist": {"src": "hda", "id": "5580169e77bda3db", "uuid": "d08e5ac9-6b04-43ac-b405-96b8cb95a1c6"}}, "update_time": "2018-02-08T17:43:45.725058", "tool_id": "mothur_heatmap_sim", "outputs": {"logfile": {"src": "hda", "id": "464746096d792407", "uuid": "bf43794a-d69f-457a-9fbc-23a419950c7c"}, "heatmap": {"src": "hda", "id": "22a2b448f3100bc3", "uuid": "dba5e528-d34f-43f6-baf2-cf6b0b10961e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > heatmap.sim(phylip=input_dist.dat,fontsize=24)\n\nOutput File Names: \ninput_dist.heatmap.sim.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1522.dat' input_dist.dat &&  echo 'heatmap.sim( phylip=input_dist.dat, fontsize=24 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:43:42.621871", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "fontsize": "\"24\"", "dbkey": "\"hg17\"", "input": "{\"source\": \"phylip\", \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 1522}]}, \"__current_case__\": 2}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "22927", "id": "4b964545b41f57a8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_heatmap_sim.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input|source": "shared", "input|otu": {"src": "hda", "id": "4265beaf3ba354f1"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "4265beaf3ba354f1", "uuid": "93279366-4f83-443c-bc00-9fb96b1d2d0e"}}, "update_time": "2018-02-08T17:44:01.685558", "tool_id": "mothur_heatmap_sim", "outputs": {"__new_primary_file_unique.thetayc.heatmap|0.15.thetayc.heatmap__": {"src": "hda", "id": "c4e4a5d9dc8d1120", "uuid": "a0adbef2-2d66-4920-9ce3-b64125941108"}, "__new_primary_file_unique.thetayc.heatmap|0.29.jest.heatmap__": {"src": "hda", "id": "180af9b3f848a9ac", "uuid": "28b31770-b932-4ba5-8759-2b02de62ddcc"}, "__new_primary_file_unique.thetayc.heatmap|0.04.thetayc.heatmap__": {"src": "hda", "id": "3586bb570babf8de", "uuid": "08bda45a-d895-4ed9-b2e3-f90932781ce8"}, "__new_primary_file_unique.thetayc.heatmap|0.18.jest.heatmap__": {"src": "hda", "id": "d3c7d1db6565c99f", "uuid": "98069c1b-96d6-4058-9e74-3f9bd14f375c"}, "__new_primary_file_unique.thetayc.heatmap|0.07.jest.heatmap__": {"src": "hda", "id": "51b118316409238c", "uuid": "2e5000b6-043f-4423-9843-c82800ca0689"}, "__new_primary_file_unique.thetayc.heatmap|0.04.jest.heatmap__": {"src": "hda", "id": "ce40f08a4c5ff084", "uuid": "1ba3d221-c019-4df6-a23d-d0e3f2d94911"}, "__new_primary_file_unique.thetayc.heatmap|0.02.jest.heatmap__": {"src": "hda", "id": "f6c11e10c580447f", "uuid": "186c5c11-8575-4bfa-88cc-91ea9233b3fb"}, "__new_primary_file_unique.thetayc.heatmap|0.01.thetayc.heatmap__": {"src": "hda", "id": "2661a717f546e3b3", "uuid": "6d4d2020-863d-40a0-9901-d66a043f8e03"}, "__new_primary_file_unique.thetayc.heatmap|0.22.thetayc.heatmap__": {"src": "hda", "id": "0f7d4a72d773ba0a", "uuid": "d652fc0c-36a6-4be2-b003-28cd245b0267"}, "__new_primary_file_unique.thetayc.heatmap|0.13.thetayc.heatmap__": {"src": "hda", "id": "fe71c2db0b5692f4", "uuid": "e9fab26d-083a-4e40-9b6f-d107e995b550"}, "__new_primary_file_unique.thetayc.heatmap|0.10.thetayc.heatmap__": {"src": "hda", "id": "97aa1ffb9ac3f2c4", "uuid": "e8f8906c-2aa3-44bc-b025-b31d0bbf7931"}, "__new_primary_file_unique.thetayc.heatmap|0.41.jest.heatmap__": {"src": "hda", "id": "6a9f6d6282ff7ad7", "uuid": "e88dcba9-34bf-47d1-a188-90c9780d5cf9"}, "__new_primary_file_unique.thetayc.heatmap|0.14.thetayc.heatmap__": {"src": "hda", "id": "30c58e9b8cdb761b", "uuid": "6ca1d288-f99b-4882-985f-3a1379038cd6"}, "__new_primary_file_unique.thetayc.heatmap|0.06.jest.heatmap__": {"src": "hda", "id": "e1f6e4d686a02e1c", "uuid": "ade3c8ad-37ec-4a19-a9bc-104c80843136"}, "__new_primary_file_unique.thetayc.heatmap|0.18.thetayc.heatmap__": {"src": "hda", "id": "f182b72ce68dba3b", "uuid": "621a6dc9-2f6c-4e7b-820a-bca58c7d0c44"}, "__new_primary_file_unique.thetayc.heatmap|0.16.jest.heatmap__": {"src": "hda", "id": "7f3108983743f974", "uuid": "5eb1910e-dc13-43e4-abe7-8efbf333aa66"}, "__new_primary_file_unique.thetayc.heatmap|0.02.thetayc.heatmap__": {"src": "hda", "id": "c1399bdeb7bb0b96", "uuid": "c1c8dc2a-b21e-4ef6-a1d1-4c62e1b866ba"}, "__new_primary_file_unique.thetayc.heatmap|0.36.thetayc.heatmap__": {"src": "hda", "id": "b17dd69ce4a6c92a", "uuid": "9c460567-673b-434e-a1b0-9274d7c9b0c6"}, 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"__new_primary_file_unique.thetayc.heatmap|0.12.jest.heatmap__": {"src": "hda", "id": "87ffab3cd82b867a", "uuid": "fe8389cf-61fc-45e6-89f8-4b73e9bc94b3"}, "__new_primary_file_unique.thetayc.heatmap|0.21.jest.heatmap__": {"src": "hda", "id": "399e6426f627a60f", "uuid": "2b4d2b38-7fad-498f-bc78-b503eb6e6ee7"}, "__new_primary_file_unique.thetayc.heatmap|0.38.jest.heatmap__": {"src": "hda", "id": "a0417eda233d5437", "uuid": "6e3123a5-3b48-4adc-b7b4-0f35656af1d4"}, "__new_primary_file_unique.thetayc.heatmap|0.05.thetayc.heatmap__": {"src": "hda", "id": "627ee27a222faba6", "uuid": "31938492-969e-488d-b50f-7048c7370452"}, "__new_primary_file_unique.thetayc.heatmap|0.22.jest.heatmap__": {"src": "hda", "id": "d375c65bcca8b11f", "uuid": "6a623a0a-11ad-42a4-a970-41d30b77fe26"}, "__new_primary_file_unique.thetayc.heatmap|0.06.thetayc.heatmap__": {"src": "hda", "id": "d81ddba20ea6fdac", "uuid": "a0bfcc9d-62c3-43ac-8696-5f24235a3cd9"}, "__new_primary_file_unique.thetayc.heatmap|0.19.jest.heatmap__": 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"__new_primary_file_unique.thetayc.heatmap|0.21.thetayc.heatmap__": {"src": "hda", "id": "b849d1f82032b54d", "uuid": "cb6ef9b7-9007-49c9-bed2-f577a0eef6ad"}, "__new_primary_file_unique.thetayc.heatmap|0.15.jest.heatmap__": {"src": "hda", "id": "6f6c68569c74f67f", "uuid": "5f1b4fe1-ab23-46fe-8080-bd09fb414b87"}, "__new_primary_file_unique.thetayc.heatmap|0.05.jest.heatmap__": {"src": "hda", "id": "229ad64670d8ad60", "uuid": "106e2022-e72e-4724-a9da-260389dbd7d8"}, "__new_primary_file_unique.thetayc.heatmap|0.23.jest.heatmap__": {"src": "hda", "id": "8faba141af95bc64", "uuid": "2c390515-c7cc-44c3-9b52-a628af36839f"}, "logfile": {"src": "hda", "id": "c29ab6099fba2aa1", "uuid": "240da7a9-44f7-4803-8e59-393ea6a33af6"}, "__new_primary_file_unique.thetayc.heatmap|0.19.thetayc.heatmap__": {"src": "hda", "id": "78b8885c8cacb5bb", "uuid": "09ec1cd6-4308-4f06-bd42-7a44624b77a7"}, "__new_primary_file_unique.thetayc.heatmap|0.29.thetayc.heatmap__": {"src": "hda", "id": "057502b1b8032dfe", "uuid": "38e93f7b-35d5-4168-b52d-3c597989b303"}, "__new_primary_file_unique.thetayc.heatmap|0.33.jest.heatmap__": {"src": "hda", "id": "7e27be0380c976f8", "uuid": "3489ff9b-0043-4a59-85e3-e369eeabf921"}, "__new_primary_file_unique.thetayc.heatmap|0.55.thetayc.heatmap__": {"src": "hda", "id": "7287d543ad977f1e", "uuid": "a5e98bc5-f7a9-46a6-8026-319d79a1fb74"}, "__new_primary_file_unique.thetayc.heatmap|0.09.jest.heatmap__": {"src": "hda", "id": "8374c09174fced28", "uuid": "da106ae4-db29-4183-940d-dbefead390ef"}, "__new_primary_file_unique.thetayc.heatmap|0.45.jest.heatmap__": {"src": "hda", "id": "ec41825bcb3c7dfe", "uuid": "fc44c5be-793d-42f1-93da-3f2896c00154"}, "__new_primary_file_unique.thetayc.heatmap|0.25.thetayc.heatmap__": {"src": "hda", "id": "f45962210a1c1b1c", "uuid": "d81d1a7e-2f35-45d3-b183-ef89b3ab9324"}, "__new_primary_file_unique.thetayc.heatmap|0.25.jest.heatmap__": {"src": "hda", "id": "6c89a539eb5e59d3", "uuid": "384b0ded-431b-47ab-a0ab-3a725ee2f9f4"}, "__new_primary_file_unique.thetayc.heatmap|0.01.jest.heatmap__": {"src": "hda", "id": "8e46a33d3b76a2b1", "uuid": "10a4cec1-dd2d-4efb-a23e-841104148bdf"}, "__new_primary_file_unique.thetayc.heatmap|0.09.thetayc.heatmap__": {"src": "hda", "id": "904e4c855c1d3c13", "uuid": "74b7344d-0914-421c-b183-c2bcfbde9595"}, "__new_primary_file_unique.thetayc.heatmap|0.32.thetayc.heatmap__": {"src": "hda", "id": "256cf1684db697f2", "uuid": "507108c1-fc03-4c9e-b50a-1c25fc53a6a8"}, "__new_primary_file_unique.thetayc.heatmap|0.08.jest.heatmap__": {"src": "hda", "id": "54383a9e773e7ce7", "uuid": "fce7e350-6d03-4bca-b12d-dc85ee273db8"}, "__new_primary_file_unique.thetayc.heatmap|0.32.jest.heatmap__": {"src": "hda", "id": "ad574be7e6b6aebd", "uuid": "088b8655-c52c-4952-9975-afe3eff2d474"}, "__new_primary_file_unique.thetayc.heatmap|0.27.jest.heatmap__": {"src": "hda", "id": "0898b95704fa8260", "uuid": "736cbf06-4db0-4135-b3ab-710884ca9b58"}, "__new_primary_file_unique.thetayc.heatmap|0.23.thetayc.heatmap__": {"src": "hda", "id": "02c68994751c0c6d", "uuid": "83a53fac-18f9-4dfa-bce8-3334153ba6c6"}, "__new_primary_file_unique.thetayc.heatmap|0.20.jest.heatmap__": {"src": "hda", "id": "fc6d8959ec51886d", "uuid": "f51dcfdb-7c93-4b3f-9268-60a1ee921c67"}, "__new_primary_file_unique.thetayc.heatmap|0.13.jest.heatmap__": {"src": "hda", "id": "310a57d95f681718", "uuid": "9c8edca0-2995-44b0-b007-b80dd1c7ad36"}, "__new_primary_file_unique.thetayc.heatmap|0.11.jest.heatmap__": {"src": "hda", "id": "9551b524a295ab47", "uuid": "6baaca63-c25b-47f2-84ec-0bc9235a0d6f"}, "__new_primary_file_unique.thetayc.heatmap|0.07.thetayc.heatmap__": {"src": "hda", "id": "5d0784c229354ea3", "uuid": "7d384e6e-a769-465a-a0be-0d79f1939c40"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > heatmap.sim(shared=input_otu.dat,calc=jest-thetayc,fontsize=24)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.unique.jest.heatmap.sim.svg\ninput_otu.unique.thetayc.heatmap.sim.svg\ninput_otu.0.01.jest.heatmap.sim.svg\ninput_otu.0.01.thetayc.heatmap.sim.svg\ninput_otu.0.02.jest.heatmap.sim.svg\ninput_otu.0.02.thetayc.heatmap.sim.svg\ninput_otu.0.03.jest.heatmap.sim.svg\ninput_otu.0.03.thetayc.heatmap.sim.svg\ninput_otu.0.04.jest.heatmap.sim.svg\ninput_otu.0.04.thetayc.heatmap.sim.svg\ninput_otu.0.05.jest.heatmap.sim.svg\ninput_otu.0.05.thetayc.heatmap.sim.svg\ninput_otu.0.06.jest.heatmap.sim.svg\ninput_otu.0.06.thetayc.heatmap.sim.svg\ninput_otu.0.07.jest.heatmap.sim.svg\ninput_otu.0.07.thetayc.heatmap.sim.svg\ninput_otu.0.08.jest.heatmap.sim.svg\ninput_otu.0.08.thetayc.heatmap.sim.svg\ninput_otu.0.09.jest.heatmap.sim.svg\ninput_otu.0.09.thetayc.heatmap.sim.svg\ninput_otu.0.10.jest.heatmap.sim.svg\ninput_otu.0.10.thetayc.heatmap.sim.svg\ninput_otu.0.11.jest.heatmap.sim.svg\ninput_otu.0.11.thetayc.heatmap.sim.svg\ninput_otu.0.12.jest.heatmap.sim.svg\ninput_otu.0.12.thetayc.heatmap.sim.svg\ninput_otu.0.13.jest.heatmap.sim.svg\ninput_otu.0.13.thetayc.heatmap.sim.svg\ninput_otu.0.14.jest.heatmap.sim.svg\ninput_otu.0.14.thetayc.heatmap.sim.svg\ninput_otu.0.15.jest.heatmap.sim.svg\ninput_otu.0.15.thetayc.heatmap.sim.svg\ninput_otu.0.16.jest.heatmap.sim.svg\ninput_otu.0.16.thetayc.heatmap.sim.svg\ninput_otu.0.17.jest.heatmap.sim.svg\ninput_otu.0.17.thetayc.heatmap.sim.svg\ninput_otu.0.18.jest.heatmap.sim.svg\ninput_otu.0.18.thetayc.heatmap.sim.svg\ninput_otu.0.19.jest.heatmap.sim.svg\ninput_otu.0.19.thetayc.heatmap.sim.svg\ninput_otu.0.20.jest.heatmap.sim.svg\ninput_otu.0.20.thetayc.heatmap.sim.svg\ninput_otu.0.21.jest.heatmap.sim.svg\ninput_otu.0.21.thetayc.heatmap.sim.svg\ninput_otu.0.22.jest.heatmap.sim.svg\ninput_otu.0.22.thetayc.heatmap.sim.svg\ninput_otu.0.23.jest.heatmap.sim.svg\ninput_otu.0.23.thetayc.heatmap.sim.svg\ninput_otu.0.24.jest.heatmap.sim.svg\ninput_otu.0.24.thetayc.heatmap.sim.svg\ninput_otu.0.25.jest.heatmap.sim.svg\ninput_otu.0.25.thetayc.heatmap.sim.svg\ninput_otu.0.26.jest.heatmap.sim.svg\ninput_otu.0.26.thetayc.heatmap.sim.svg\ninput_otu.0.27.jest.heatmap.sim.svg\ninput_otu.0.27.thetayc.heatmap.sim.svg\ninput_otu.0.29.jest.heatmap.sim.svg\ninput_otu.0.29.thetayc.heatmap.sim.svg\ninput_otu.0.32.jest.heatmap.sim.svg\ninput_otu.0.32.thetayc.heatmap.sim.svg\ninput_otu.0.33.jest.heatmap.sim.svg\ninput_otu.0.33.thetayc.heatmap.sim.svg\ninput_otu.0.36.jest.heatmap.sim.svg\ninput_otu.0.36.thetayc.heatmap.sim.svg\ninput_otu.0.38.jest.heatmap.sim.svg\ninput_otu.0.38.thetayc.heatmap.sim.svg\ninput_otu.0.41.jest.heatmap.sim.svg\ninput_otu.0.41.thetayc.heatmap.sim.svg\ninput_otu.0.45.jest.heatmap.sim.svg\ninput_otu.0.45.thetayc.heatmap.sim.svg\ninput_otu.0.55.jest.heatmap.sim.svg\ninput_otu.0.55.thetayc.heatmap.sim.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1525.dat' input_otu.dat &&  echo 'heatmap.sim( shared=input_otu.dat, calc=jest-thetayc, fontsize=24 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:43:55.214842", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "fontsize": "\"24\"", "dbkey": "\"hg17\"", "input": "{\"__current_case__\": 0, \"label\": null, \"source\": \"shared\", \"groups\": null, \"calc\": [\"jest\", \"thetayc\"], \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1525}]}}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23014", "id": "732b43bd12cd060f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_heatmap_sim.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input|label": ["0.03", "0.26", "0.55"], "input|source": "shared", "input|groups": ["forest", "pasture"], "input|calc": ["jclass", "jest", "sorclass", "sorest", "braycurtis", "jabund", "morisitahorn", "sorabund", "thetan", "thetayc"], "input|otu": {"src": "hda", "id": "0e4b67279a0941db"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "0e4b67279a0941db", "uuid": "9f549eac-d1a5-4fde-b3e9-902bf0757f61"}}, "update_time": "2018-02-08T17:44:17.923624", "tool_id": "mothur_heatmap_sim", "outputs": {"__new_primary_file_0.55.thetayc.heatmap|0.55.thetayc.heatmap__": {"src": "hda", "id": "97a1fd4764430d7d", "uuid": "126f6a6b-71ae-461c-8af1-bd714fd0f4ff"}, "__new_primary_file_0.55.thetayc.heatmap|0.26.sorclass.heatmap__": {"src": "hda", "id": "440b08187b03ca78", "uuid": "2212efa2-29d8-48e5-9554-6f46f4d98ba0"}, "__new_primary_file_0.55.thetayc.heatmap|0.26.morisitahorn.heatmap__": {"src": "hda", "id": "f7a22a56bf98efba", "uuid": "5f04e2bd-1506-469f-a5c8-b9a78e689794"}, "__new_primary_file_0.55.thetayc.heatmap|0.26.jclass.heatmap__": {"src": "hda", "id": "fb48ee8a404d26a9", "uuid": "96252991-ed2c-4dc1-a35a-fac17f6d68c7"}, "__new_primary_file_0.55.thetayc.heatmap|0.03.sorclass.heatmap__": {"src": "hda", "id": "6200b6b6e3e5d3c6", "uuid": "f61f9ef6-d00f-4e6c-ba5e-c0349ccbf8c3"}, "__new_primary_file_0.55.thetayc.heatmap|0.26.jest.heatmap__": {"src": "hda", "id": "dfb5acc45c9e0393", "uuid": "32d7bbb8-b78c-4994-b5fd-f372bb4f1c54"}, "__new_primary_file_0.55.thetayc.heatmap|0.55.jclass.heatmap__": {"src": "hda", "id": "4b0dcf789f89250e", "uuid": "c26de56e-5a88-454e-bd5f-851684f97089"}, "__new_primary_file_0.55.thetayc.heatmap|0.55.sorabund.heatmap__": {"src": "hda", "id": "44753ae8c747323a", "uuid": "17bbbdb5-5e8a-493f-ac86-0f2a497e30d4"}, "__new_primary_file_0.55.thetayc.heatmap|0.03.jclass.heatmap__": {"src": "hda", "id": "129ec904eaa7b025", "uuid": "e8f0c5ba-aa74-485c-8699-0643928426c4"}, "__new_primary_file_0.55.thetayc.heatmap|0.26.sorest.heatmap__": {"src": "hda", "id": "ba44e50454176a40", "uuid": "1bd9af92-9e25-4124-9d7c-9fa25049917d"}, "__new_primary_file_0.55.thetayc.heatmap|0.03.jest.heatmap__": {"src": "hda", "id": "3e552153c1355876", "uuid": "8ae431b0-596d-4231-8931-ef31e7a9ad93"}, "__new_primary_file_0.55.thetayc.heatmap|0.03.thetayc.heatmap__": {"src": "hda", "id": "bf8f97fc9d2f53ad", "uuid": "78cda9a8-caff-4203-a1ef-63d0a5401087"}, "__new_primary_file_0.55.thetayc.heatmap|0.26.braycurtis.heatmap__": {"src": "hda", "id": "52db18947e82628a", "uuid": "0dfee0e6-4d0d-4f37-b508-1adc585653c2"}, "__new_primary_file_0.55.thetayc.heatmap|0.55.sorclass.heatmap__": {"src": "hda", "id": "6617d9e33373df14", "uuid": "a07948d5-4788-4678-ac13-cd8ada7bc7ef"}, "__new_primary_file_0.55.thetayc.heatmap|0.26.sorabund.heatmap__": {"src": "hda", "id": "cadc96473f17a847", "uuid": "ec06c187-085e-46a5-be15-7fca21df5c1b"}, "__new_primary_file_0.55.thetayc.heatmap|0.55.sorest.heatmap__": {"src": "hda", "id": "182f3c5e367f21ec", "uuid": "c76d1bf0-d70f-464a-90d8-ee4f478bf5d9"}, "__new_primary_file_0.55.thetayc.heatmap|0.55.braycurtis.heatmap__": {"src": "hda", "id": "bfac8aa31a378884", "uuid": "c2d763e8-133a-466d-92eb-34c36f49daf5"}, "__new_primary_file_0.55.thetayc.heatmap|0.55.jabund.heatmap__": {"src": "hda", "id": "be5c34656f56b1c8", "uuid": "bc8ea17e-e3fc-42f0-bc96-701c251b60d4"}, "__new_primary_file_0.55.thetayc.heatmap|0.55.thetan.heatmap__": {"src": "hda", "id": "2c5c4a8381427e09", "uuid": "3e06e985-5947-4712-a497-833166777c18"}, "__new_primary_file_0.55.thetayc.heatmap|0.03.morisitahorn.heatmap__": {"src": "hda", "id": "126bd5267c0c550c", "uuid": "52d36d37-f428-4e08-823f-9e7fd64a76f8"}, "__new_primary_file_0.55.thetayc.heatmap|0.03.jabund.heatmap__": {"src": "hda", "id": "3adfe7a97cdc075a", "uuid": "2f4025aa-70f6-4987-9c60-cd38135a6eeb"}, "logfile": {"src": "hda", "id": "685dd60bfbef3aba", "uuid": "888d07e6-9a26-4129-8dcc-e6f10c65b9c1"}, "__new_primary_file_0.55.thetayc.heatmap|0.55.jest.heatmap__": {"src": "hda", "id": "f8e11f8ada66d0f4", "uuid": "63b80517-8fd4-463a-906f-38c5fba20338"}, "__new_primary_file_0.55.thetayc.heatmap|0.03.sorabund.heatmap__": {"src": "hda", "id": "1dc9e2614ae44c6f", "uuid": "10c8d90e-58dd-4bf2-837e-a9f3e6a08850"}, "__new_primary_file_0.55.thetayc.heatmap|0.26.thetayc.heatmap__": {"src": "hda", "id": "9e4e9d5b1a0ea25c", "uuid": "b7db93e8-7e24-466b-a3cd-4c245586d39b"}, "__new_primary_file_0.55.thetayc.heatmap|0.55.morisitahorn.heatmap__": {"src": "hda", "id": "1223008bb03781ea", "uuid": "d9e21b06-1794-4676-8d9f-ceb098994400"}, "__new_primary_file_0.55.thetayc.heatmap|0.03.thetan.heatmap__": {"src": "hda", "id": "a3a1edb65ca58d52", "uuid": "f90d3ab8-422e-4aa5-b443-773503c56691"}, "__new_primary_file_0.55.thetayc.heatmap|0.26.thetan.heatmap__": {"src": "hda", "id": "3d67993e78966025", "uuid": "dc62680a-b693-4256-a475-f78fb1a093cd"}, "__new_primary_file_0.55.thetayc.heatmap|0.03.sorest.heatmap__": {"src": "hda", "id": "4e3fce0b8fcfe562", "uuid": "d7e5d7ec-d097-4d9e-9852-04dc3bb3739a"}, "__new_primary_file_0.55.thetayc.heatmap|0.26.jabund.heatmap__": {"src": "hda", "id": "32fa0d439185428a", "uuid": "b55bd189-b583-4b1a-9325-399734daadcd"}, "__new_primary_file_0.55.thetayc.heatmap|0.03.braycurtis.heatmap__": {"src": "hda", "id": "b46a645fa458e7c7", "uuid": "f8aa1f3c-bb6f-400c-905a-1ee7ff72a4b8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > heatmap.sim(shared=input_otu.dat,label=0.03-0.26-0.55,groups=forest-pas \rture,calc=jclass-jest-sorclass-sorest-braycurtis-jabund-morisitahorn-sorabund-th \retan-thetayc,fontsize=24)\n0.03\n0.26\n0.55\n\nOutput File Names: \ninput_otu.0.03.jclass.heatmap.sim.svg\ninput_otu.0.03.jest.heatmap.sim.svg\ninput_otu.0.03.sorclass.heatmap.sim.svg\ninput_otu.0.03.sorest.heatmap.sim.svg\ninput_otu.0.03.braycurtis.heatmap.sim.svg\ninput_otu.0.03.jabund.heatmap.sim.svg\ninput_otu.0.03.morisitahorn.heatmap.sim.svg\ninput_otu.0.03.sorabund.heatmap.sim.svg\ninput_otu.0.03.thetan.heatmap.sim.svg\ninput_otu.0.03.thetayc.heatmap.sim.svg\ninput_otu.0.26.jclass.heatmap.sim.svg\ninput_otu.0.26.jest.heatmap.sim.svg\ninput_otu.0.26.sorclass.heatmap.sim.svg\ninput_otu.0.26.sorest.heatmap.sim.svg\ninput_otu.0.26.braycurtis.heatmap.sim.svg\ninput_otu.0.26.jabund.heatmap.sim.svg\ninput_otu.0.26.morisitahorn.heatmap.sim.svg\ninput_otu.0.26.sorabund.heatmap.sim.svg\ninput_otu.0.26.thetan.heatmap.sim.svg\ninput_otu.0.26.thetayc.heatmap.sim.svg\ninput_otu.0.55.jclass.heatmap.sim.svg\ninput_otu.0.55.jest.heatmap.sim.svg\ninput_otu.0.55.sorclass.heatmap.sim.svg\ninput_otu.0.55.sorest.heatmap.sim.svg\ninput_otu.0.55.braycurtis.heatmap.sim.svg\ninput_otu.0.55.jabund.heatmap.sim.svg\ninput_otu.0.55.morisitahorn.heatmap.sim.svg\ninput_otu.0.55.sorabund.heatmap.sim.svg\ninput_otu.0.55.thetan.heatmap.sim.svg\ninput_otu.0.55.thetayc.heatmap.sim.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1599.dat' input_otu.dat &&  echo 'heatmap.sim( shared=input_otu.dat, label=0.03-0.26-0.55, groups=forest-pasture, calc=jclass-jest-sorclass-sorest-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc, fontsize=24 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:44:13.381299", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "fontsize": "\"24\"", "dbkey": "\"hg17\"", "input": "{\"__current_case__\": 0, \"label\": [\"0.03\", \"0.26\", \"0.55\"], \"source\": \"shared\", \"groups\": [\"forest\", \"pasture\"], \"calc\": [\"jclass\", \"jest\", \"sorclass\", \"sorest\", \"braycurtis\", \"jabund\", \"morisitahorn\", \"sorabund\", \"thetan\", \"thetayc\"], \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1599}]}}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23100", "id": "b7d5085eacaa6509", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_heatmap_sim.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"design": {"src": "hda", "id": "b75e6fd397636254"}, "dist": {"src": "hda", "id": "e781318b8db2a130"}}, "job": {"inputs": {"design": {"src": "hda", "id": "b75e6fd397636254", "uuid": "85c2ef82-3edd-4628-a8e1-83ee3078e9a2"}, "dist": {"src": "hda", "id": "e781318b8db2a130", "uuid": "6e3fccba-a0be-4020-9c3f-a1d7b22edff5"}}, "update_time": "2018-02-08T17:44:35.076991", "tool_id": "mothur_homova", "outputs": {"logfile": {"src": "hda", "id": "c27f325b0d5006b2", "uuid": "e59ee541-7405-47a1-a60c-100b5add88ed"}, "homova": {"src": "hda", "id": "05bd3a5145917735", "uuid": "90841dd8-01d4-4ef1-9c98-8705de5cc4d2"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > homova(phylip=dist.dat,design=design.dat,iters=1000,alpha=0.05)\nHOMOVA\tBValue\tP-value\tSSwithin/(Ni-1)_values\nA-B\t0.000158784\t0.983\t0.0491681\t0.0493482\nExperiment-wise error rate: 0.05\nIf you have borderline P-values, you should try increasing the number of iterations\n\nOutput File Names: \ndist.homova\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1631.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1632.dat' design.dat &&  echo 'homova( phylip=dist.dat, design=design.dat, iters=1000, alpha=0.05 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:44:31.897262", "params": {"iters": "\"1000\"", "alpha": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "sets": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23208", "id": "7535296d23a37c60", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_homova.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"design": {"src": "hda", "id": "e3dee98f1c9649e3"}, "dist": {"src": "hda", "id": "633b54cb360cf9db"}, "sets": "A"}, "job": {"inputs": {"design": {"src": "hda", "id": "e3dee98f1c9649e3", "uuid": "908ca6b1-8c4c-4bea-a596-bdd91b839874"}, "dist": {"src": "hda", "id": "633b54cb360cf9db", "uuid": "deaecaee-ec95-4c03-b244-25f26b281919"}}, "update_time": "2018-02-08T17:44:55.739229", "tool_id": "mothur_homova", "outputs": {"logfile": {"src": "hda", "id": "c1fddc7a0d53eefd", "uuid": "e0ce6399-ff67-4c22-8cea-e623fe3b0216"}, "homova": {"src": "hda", "id": "d0a2e604f819e3c6", "uuid": "45572e52-1c5d-4123-a010-8850c8842c1f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > homova(phylip=dist.dat,design=design.dat,sets=A,iters=1000,alpha=0.05)\nHOMOVA\tBValue\tP-value\tSSwithin/(Ni-1)_values\nA\t-nan\t<0.001*\t0.0491681\nExperiment-wise error rate: 0.05\nIf you have borderline P-values, you should try increasing the number of iterations\n\nOutput File Names: \ndist.homova\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1635.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1636.dat' design.dat &&  echo 'homova( phylip=dist.dat, design=design.dat, sets=A, iters=1000, alpha=0.05 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:44:52.539310", "params": {"iters": "\"1000\"", "alpha": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "sets": "\"A\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23326", "id": "957dec9f2200cbe4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_homova.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"withdesign|design": {"src": "hda", "id": "130add1cdbd710d8"}, "withdesign|groups": ["tardis", "dalek"], "withdesign|havedesign": "yes", "otu": {"src": "hda", "id": "71da8dd0f551f579"}, "label": "0.03"}, "job": {"inputs": {"design": {"src": "hda", "id": "130add1cdbd710d8", "uuid": "15911e5f-c171-4f42-9061-2f65d9e9a6e9"}, "otu": {"src": "hda", "id": "71da8dd0f551f579", "uuid": "4b9303dd-3e4b-4e6c-bf6d-33a8c6c28a87"}}, "update_time": "2018-02-08T17:45:16.789870", "tool_id": "mothur_indicator", "outputs": {"logfile": {"src": "hda", "id": "d3ae0c1d73470c9e", "uuid": "adfe74af-d747-4106-b553-74dfadcd5ede"}, "tree_out": {"src": "hda", "id": "b9f3ee2dd66df0a7", "uuid": "61fd6af0-ad22-457c-a4f2-00514ead459f"}, "summary": {"src": "hda", "id": "b84330ef16365123", "uuid": "747d571a-41a4-4dd5-b004-e17b52e62210"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > indicator(shared=otu.dat,label=0.03,groups=tardis-dalek,design=withdesi \rgn.design.dat,processors=1)\n\nUsing 1 processors.\n\nSpecies\tIndicator_Groups\tIndicatorValue\tpValue\n\n\nIt took 0 secs to find the indicator species.\n\nOutput File Names: \notu.indicator.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1639.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1640.dat' withdesign.design.dat &&  echo 'indicator( shared=otu.dat, label=0.03, groups=tardis-dalek, design=withdesign.design.dat, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:45:13.218298", "params": {"withdesign": "{\"design\": {\"values\": [{\"src\": \"hda\", \"id\": 1640}]}, \"havedesign\": \"yes\", \"tree\": null, \"groups\": [\"tardis\", \"dalek\"], \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "\"0.03\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23436", "id": "c809b2abaed97358", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_indicator.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"withdesign|design": {"src": "hda", "id": "4d319bb7f31107cc"}, "withdesign|groups": "tardis", "otu": {"src": "hda", "id": "f291c23df814c8b2"}, "withdesign|havedesign": "yes"}, "job": {"inputs": {"design": {"src": "hda", "id": "4d319bb7f31107cc", "uuid": "f27eeb67-8afe-41c7-9c05-b619f5699688"}, "otu": {"src": "hda", "id": "f291c23df814c8b2", "uuid": "4b43aa5e-f1ee-497c-b108-5893d1f1a355"}}, "update_time": "2018-02-08T17:45:34.981694", "tool_id": "mothur_indicator", "outputs": {"logfile": {"src": "hda", "id": "0922d58fdca8782c", "uuid": "17ecbb2f-8aa3-4c45-9ee4-3148e749c893"}, "tree_out": {"src": "hda", "id": "358ee0efc1019ede", "uuid": "138af667-fb25-48f8-9b46-c4fe6b8c111c"}, "summary": {"src": "hda", "id": "b2b3ae4f6b3403ef", "uuid": "60c99c02-357b-44aa-98a6-e84288ae1b33"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > indicator(shared=otu.dat,groups=tardis,design=withdesign.design.dat,pro \rcessors=1)\nYou did not provide a label, I will use the first label in your inputfile.\n\nUsing 1 processors.\n\nSpecies\tIndicator_Groups\tIndicatorValue\tpValue\n\n\nIt took 0 secs to find the indicator species.\n\nOutput File Names: \notu.indicator.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1644.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1645.dat' withdesign.design.dat &&  echo 'indicator( shared=otu.dat, groups=tardis, design=withdesign.design.dat, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:45:31.778529", "params": {"withdesign": "{\"design\": {\"values\": [{\"src\": \"hda\", \"id\": 1645}]}, \"havedesign\": \"yes\", \"tree\": null, \"groups\": \"tardis\", \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23575", "id": "63f8201b30d2cadd", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_indicator.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"withdesign|tree": {"src": "hda", "id": "cf368cb6bca06f2e"}, "withdesign|groups": ["forest", "pasture"], "otu": {"src": "hda", "id": "34863713120b282b"}, "withdesign|havedesign": "no"}, "job": {"inputs": {"tree": {"src": "hda", "id": "cf368cb6bca06f2e", "uuid": "fb91c6ca-5179-40d5-942b-9c0c41f565fe"}, "otu": {"src": "hda", "id": "34863713120b282b", "uuid": "a64db36f-188c-4ce3-aba8-b472e74488c1"}}, "update_time": "2018-02-08T17:45:51.764425", "tool_id": "mothur_indicator", "outputs": {"logfile": {"src": "hda", "id": "f90ecd13a46a1b7b", "uuid": "7c6a2d9d-ff55-4330-a2f1-353f525891a6"}, "tree_out": {"src": "hda", "id": "a7092c007b7a86a3", "uuid": "a828a14e-a4a1-4644-997f-34b2cd26c085"}, "summary": {"src": "hda", "id": "463c07f914921351", "uuid": "aed53623-3451-4cf4-8bdd-10ee5d8cc381"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > indicator(tree=withdesign.tree.dat,shared=otu.dat,groups=forest-pasture \r,processors=1)\nYou did not provide a label, I will use the first label in your inputfile.\n\nUsing 1 processors.\n\nNode\tSpecies\tIndicator_Groups\tIndicatorValue\tpValue\n\n\nIt took 0 secs to find the indicator species.\n\nOutput File Names: \notu.indicator.summary\nwithdesign.tree.indicator.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1649.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1650.dat' withdesign.tree.dat &&  echo 'indicator( tree=withdesign.tree.dat, shared=otu.dat, groups=forest-pasture, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:45:48.263076", "params": {"withdesign": "{\"havedesign\": \"no\", \"tree\": {\"values\": [{\"src\": \"hda\", \"id\": 1650}]}, \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23689", "id": "9c8aa3de76c5f0c4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_indicator.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"withdesign|tree": {"src": "hda", "id": "07756f5d8c72ca12"}, "withdesign|groups": "forest", "otu": {"src": "hda", "id": "52ebed6720d1663f"}, "withdesign|havedesign": "no"}, "job": {"inputs": {"tree": {"src": "hda", "id": "07756f5d8c72ca12", "uuid": "42c5f9ab-da25-4bd9-a714-f936b4738249"}, "otu": {"src": "hda", "id": "52ebed6720d1663f", "uuid": "77cd1cf9-2422-43c7-9e19-0030139b8dd6"}}, "update_time": "2018-02-08T17:46:10.011812", "tool_id": "mothur_indicator", "outputs": {"logfile": {"src": "hda", "id": "d5612dcbb5ce0366", "uuid": "fdb6bfce-1f1e-4b99-946a-998aa250c4eb"}, "tree_out": {"src": "hda", "id": "bf85d0c93ded3f21", "uuid": "4235f8b7-f464-457a-8eb2-54a0c6560517"}, "summary": {"src": "hda", "id": "84981bc5aab6e32e", "uuid": "604c93ea-ba6b-4c62-b777-8c1fbbd52fc7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > indicator(tree=withdesign.tree.dat,shared=otu.dat,groups=forest,process \rors=1)\nYou did not provide a label, I will use the first label in your inputfile.\n\nUsing 1 processors.\n\nNode\tSpecies\tIndicator_Groups\tIndicatorValue\tpValue\n\n\nIt took 0 secs to find the indicator species.\n\nOutput File Names: \notu.indicator.summary\nwithdesign.tree.indicator.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1654.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1655.dat' withdesign.tree.dat &&  echo 'indicator( tree=withdesign.tree.dat, shared=otu.dat, groups=forest, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:46:06.809366", "params": {"withdesign": "{\"havedesign\": \"no\", \"tree\": {\"values\": [{\"src\": \"hda\", \"id\": 1655}]}, \"groups\": \"forest\", \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23799", "id": "3529226cbbc41f8d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_indicator.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"design": {"src": "hda", "id": "4c8788abad1b338d"}, "otu": {"src": "hda", "id": "ea73bab1c36fe6e9"}}, "job": {"inputs": {"design": {"src": "hda", "id": "4c8788abad1b338d", "uuid": "76ccc0a4-267f-42e0-8370-c8833609cf74"}, "otu": {"src": "hda", "id": "ea73bab1c36fe6e9", "uuid": "3ae7682f-ce62-4425-b388-004af01134e7"}}, "update_time": "2018-02-08T17:46:26.299101", "tool_id": "mothur_lefse", "outputs": {"logfile": {"src": "hda", "id": "db96ea5535812b22", "uuid": "c2965e21-4799-42a6-aca3-7a0095ede7cc"}, "summary": {"src": "hda", "id": "a62d77069d50a785", "uuid": "f4d010af-638e-4311-8a51-e32990abbb71"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > lefse(shared=shared.dat,design=design.dat,aalpha=0.05,walpha=0.05,lda=2 \r.0,iters=30,fboots=0.67,strict=0,minc=10,wilc=T,curv=F,norm=T)\n\nYou did not provide a class, using dpw.\n\n1\n\nNumber of significantly discriminative features: 0 ( 0 ) before internal wilcoxon.\nNo features with significant differences between the classes.\n\nOutput File Names: \nshared.1.lefse_summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1659.dat' shared.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1660.dat' design.dat &&  echo 'lefse( shared=shared.dat, design=design.dat, aalpha=0.05, walpha=0.05, lda=2.0, iters=30, fboots=0.67, strict=0, minc=10, wilc=T, curv=F, norm=T )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:46:23.249880", "params": {"curv": "\"false\"", "aalpha": "\"0.05\"", "lda": "\"2.0\"", "sclass": "\"\"", "iters": "\"30\"", "minc": "\"10\"", "dbkey": "\"hg17\"", "label": "null", "strict": "\"0\"", "fboots": "\"0.67\"", "walpha": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "class": "\"\"", "norm": "\"true\"", "wilc": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "23913", "id": "c397987c596ee46a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_lefse.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"design": {"src": "hda", "id": "f2cb52eef4673733"}, "class": "dpw", "otu": {"src": "hda", "id": "e6bcd3f9b805457c"}, "label": "1"}, "job": {"inputs": {"design": {"src": "hda", "id": "f2cb52eef4673733", "uuid": "ce83be1e-e3f2-4832-9354-072e95c02005"}, "otu": {"src": "hda", "id": "e6bcd3f9b805457c", "uuid": "4a9e038b-4c1d-43ed-b0dc-956d4100cc25"}}, "update_time": "2018-02-08T17:46:47.849034", "tool_id": "mothur_lefse", "outputs": {"logfile": {"src": "hda", "id": "41697c66808448c5", "uuid": "0823ce30-2352-4a24-b35b-46a5ed46bc1e"}, "summary": {"src": "hda", "id": "cc3d3fc6d6226aa1", "uuid": "e66dff78-5bd6-43bb-b0ab-e1a54d06b08a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > lefse(shared=shared.dat,design=design.dat,class=dpw,label=1,aalpha=0.05 \r,walpha=0.05,lda=2.0,iters=30,fboots=0.67,strict=0,minc=10,wilc=T,curv=F,norm=T) \r\u001b[A\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[K)\n1\n\nNumber of significantly discriminative features: 0 ( 0 ) before internal wilcoxon.\nNo features with significant differences between the classes.\n\nOutput File Names: \nshared.1.lefse_summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1663.dat' shared.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1664.dat' design.dat &&  echo 'lefse( shared=shared.dat, design=design.dat, class=dpw, label=1, aalpha=0.05, walpha=0.05, lda=2.0, iters=30, fboots=0.67, strict=0, minc=10, wilc=T, curv=F, norm=T )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:46:44.723129", "params": {"curv": "\"false\"", "aalpha": "\"0.05\"", "lda": "\"2.0\"", "sclass": "\"\"", "iters": "\"30\"", "minc": "\"10\"", "dbkey": "\"hg17\"", "label": "\"1\"", "strict": "\"0\"", "fboots": "\"0.67\"", "walpha": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "class": "\"dpw\"", "norm": "\"true\"", "wilc": "\"true\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24029", "id": "f5edea7d52e42cd6", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_lefse.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "0af819d9e24eaa3e"}, "dist": {"src": "hda", "id": "09113d1870481726"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "09113d1870481726", "uuid": "5e9fd652-9864-48b9-a417-84a2afbcc375"}, "group": {"src": "hda", "id": "0af819d9e24eaa3e", "uuid": "2b23b0a7-96d9-4071-8c1a-a0d7c8e928ef"}}, "update_time": "2018-02-08T17:47:08.945526", "tool_id": "mothur_libshuff", "outputs": {"logfile": {"src": "hda", "id": "9a1d171d0e8eec98", "uuid": "28c0ee7e-69ee-48db-bda5-a8027c01c303"}, "coverage": {"src": "hda", "id": "cb463262cf10668c", "uuid": "91c4a6f2-c515-46c9-8348-65e34bc4d41f"}, "summary": {"src": "hda", "id": "ef6796f5d6fc008a", "uuid": "916bb2ff-845b-497b-a28e-9dfc1b69a58a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > libshuff(phylip=dist.dat,group=group.dat,sim=false,iters=10000)\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n********************#****#****#****#****#****#****#****#****#****#****#\nforest-pasture      ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nComparison          \tdCXYScore\tSignificance\n\nforest-pasture      \t0.00500262\t0.0098\n\npasture-forest      \t0.00289600\t0.0625\n\n\nOutput File Names: \ndist.libshuff.summary\ndist.libshuff.coverage\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1667.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1668.dat' group.dat &&  echo 'libshuff( phylip=dist.dat, group=group.dat, sim=false, iters=10000 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:47:05.439444", "params": {"form": "{\"form2\": \"integral\", \"__current_case__\": 0}", "iters": "\"10000\"", "dbkey": "\"hg17\"", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "sim": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24148", "id": "e6b222c9649e44d2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_libshuff.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"form|form2": "discrete", "dist": {"src": "hda", "id": "1c7735ec1b73fbb8"}, "groups": ["forest", "pasture"], "group": {"src": "hda", "id": "1616a3130c86f35d"}, "form|cutoff": "0.25", "form|step": "0.25"}, "job": {"inputs": {"dist": {"src": "hda", "id": "1c7735ec1b73fbb8", "uuid": "46fd625d-9858-41ff-bdfa-5bc20ff40823"}, "group": {"src": "hda", "id": "1616a3130c86f35d", "uuid": "fbf06a31-6643-4fc8-bf56-ed4bd0ca8e3e"}}, "update_time": "2018-02-08T17:47:27.398142", "tool_id": "mothur_libshuff", "outputs": {"logfile": {"src": "hda", "id": "af6859f1d0663d97", "uuid": "1f3ac1e6-70fd-450e-8bf0-0513298e6b9d"}, "coverage": {"src": "hda", "id": "79fc5e356a32badd", "uuid": "0f4f377a-5ab6-471e-9623-c7bf16bab1cf"}, "summary": {"src": "hda", "id": "3161fe67334a087c", "uuid": "99b3061a-4061-46a7-935b-6151908ee0ad"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > libshuff(phylip=dist.dat,group=group.dat,groups=forest-pasture,sim=fals \re,step=0.25,cutoff=0.25,iters=10000)\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n********************#****#****#****#****#****#****#****#****#****#****#\nforest-pasture      ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nComparison          \tdCXYScore\tSignificance\n\nforest-pasture      \t0.00500262\t0.0086\n\npasture-forest      \t0.00289600\t0.0615\n\n\nOutput File Names: \ndist.libshuff.summary\ndist.libshuff.coverage\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1672.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1673.dat' group.dat &&  echo 'libshuff( phylip=dist.dat, group=group.dat, groups=forest-pasture, sim=false, step=0.25, cutoff=0.25, iters=10000 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:47:23.914400", "params": {"form": "{\"form2\": \"discrete\", \"step\": \"0.25\", \"__current_case__\": 1, \"cutoff\": \"0.25\"}", "iters": "\"10000\"", "dbkey": "\"hg17\"", "groups": "[\"forest\", \"pasture\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "sim": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24259", "id": "6eb09fe0ca80e9ad", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_libshuff.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "03515b901bb7065c"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "03515b901bb7065c", "uuid": "7d8f0902-b27b-482b-b7b2-68062efece02"}}, "update_time": "2018-02-08T17:47:44.898090", "tool_id": "mothur_list_otulabels", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "1d124e18e52f63d6", "uuid": "43571c49-d01e-49dd-b357-784a688b67b7"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "e4eea0d00dd11fc1", "uuid": "3bc47209-507b-4bef-a09e-2a470838ddf3"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "0f127131f3eb2bfd", "uuid": "f479223f-8830-4086-adec-517a1bbe14cf"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "e98378c72dd331ce", "uuid": "c303d2bf-1895-46f0-aa12-a075667eacd8"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "102e4f978a39c67b", "uuid": "c57020f8-a106-4414-84b1-8c90cddfe6fb"}, "__new_primary_file_unique|0.16__": {"src": "hda", "id": "511779d6bc9751e8", "uuid": "b545984e-ffbb-4573-8967-34a02064b17c"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "da0dba679b1ff231", "uuid": "09097db4-4139-4801-b08f-9eaf37d6ebce"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "dfc4bdd80e844267", "uuid": "d976179c-5b00-45e2-849b-be48d3768b0f"}, "__new_primary_file_unique|0.15__": {"src": "hda", "id": "29e2d6771c60c803", "uuid": "39c4051b-8b46-453e-84d7-f3bc7779c936"}, "__new_primary_file_unique|0.08__": {"src": "hda", "id": "1f6c0bf0abda3a36", "uuid": "5f97d8d5-7362-4f87-b5fb-3755e0f8e3b7"}, "__new_primary_file_unique|0.14__": {"src": "hda", "id": "046c583ea67d56fe", "uuid": "fc632040-56b9-47b0-8cff-625533d47792"}, "__new_primary_file_unique|0.13__": {"src": "hda", "id": "6d3f04dcd4f83b40", "uuid": "dfaffc5e-216d-4867-91a6-25370405386f"}, "__new_primary_file_unique|0.09__": {"src": "hda", "id": "bac292913e61351f", "uuid": "703444c0-9ba6-4550-b52b-3b20d36cd2cb"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "6c240f6767045bc7", "uuid": "7923dc0a-8dc7-4e53-aaf9-007771a94681"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "5d51f2eb28447d68", "uuid": "ff23e7fb-20d5-4922-8750-a01fe8aaa1a3"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "9efd53024480d419", "uuid": "18440ce6-14b8-4ba0-9a30-bc4897ee117f"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "5cee183d473e5065", "uuid": "fb9b3b63-f9fa-4dff-b85c-c2073fc04577"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "8ae7d654d115358b", "uuid": "0bdbe523-7a38-4898-bf1d-7b6ea5a81f9c"}, "__new_primary_file_unique|0.25__": {"src": "hda", "id": "071905bbb8e343b5", "uuid": "8bddde77-2e1a-48c3-8194-396b5ab2af56"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "3e4dfa0ba4528210", "uuid": "89788c08-81a1-44d7-894f-cf9117672a38"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "207deb3ab3773d6e", "uuid": "032b2031-ad18-4990-b85a-2f7a69664241"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "4d7e2d7680b0f930", "uuid": "45702390-3a68-43d6-8611-7fa08fceab0c"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "ee5577484782be17", "uuid": "f6d7b004-22f6-4c71-973b-59a4b9d42703"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "9f1be559dcee58e4", "uuid": "338d2719-bd3a-4314-823e-fc375345a4cf"}, "logfile": {"src": "hda", "id": "eabc8b40ba5517ea", "uuid": "52bd6bf7-6519-4db6-90d9-2e94bd5cebea"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "84978e4e99593596", "uuid": "7159457d-d852-4043-a553-f6203c785eb6"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "791caff901bcced2", "uuid": "5d5663aa-90f1-4dd1-bcc3-7d75f5f1d512"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "a254ed162f2c861f", "uuid": "5449536b-602f-4cb2-b7f4-962f6ef68935"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "da52058ee935cacf", "uuid": "0510615d-706e-4a59-941a-42f81914f237"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "e42a943db0671336", "uuid": "e5f093e3-26e9-41eb-8a2f-b498242c876f"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "0f9af512d4e9c186", "uuid": "c8c56ede-3e49-41dc-a259-dafffc9cec14"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "9dd182eaaac31990", "uuid": "20386d9f-3bf1-4fb6-852f-8ff182f333df"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "566a42aa096b25c3", "uuid": "27d523b1-85da-4fc9-afa6-1dbbe5aec3f7"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "98d05f669e70824c", "uuid": "107b9482-ee08-47a5-83f0-4f1dc6429926"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "5d7f51f61764264a", "uuid": "9f25bddf-d98f-4a32-84c9-49bd1cb35377"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "94c8505ae27068a3", "uuid": "6d194638-4392-4ff1-a076-62bd7235a064"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "fdb3c5bd15bc0651", "uuid": "780b8b1b-3593-4a03-acf9-b0b75bd52b24"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > list.otulabels(list=otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.otulabels\notu.0.01.otulabels\notu.0.02.otulabels\notu.0.03.otulabels\notu.0.04.otulabels\notu.0.05.otulabels\notu.0.06.otulabels\notu.0.07.otulabels\notu.0.08.otulabels\notu.0.09.otulabels\notu.0.10.otulabels\notu.0.11.otulabels\notu.0.12.otulabels\notu.0.13.otulabels\notu.0.14.otulabels\notu.0.15.otulabels\notu.0.16.otulabels\notu.0.17.otulabels\notu.0.18.otulabels\notu.0.19.otulabels\notu.0.20.otulabels\notu.0.21.otulabels\notu.0.22.otulabels\notu.0.23.otulabels\notu.0.24.otulabels\notu.0.25.otulabels\notu.0.26.otulabels\notu.0.27.otulabels\notu.0.29.otulabels\notu.0.32.otulabels\notu.0.33.otulabels\notu.0.36.otulabels\notu.0.38.otulabels\notu.0.41.otulabels\notu.0.45.otulabels\notu.0.55.otulabels\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1677.dat' otu.dat &&  echo 'list.otulabels( list=otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:47:40.035318", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "null", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24355", "id": "09dbeac489d85549", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_list_otulabels.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "7ce5ee5ae5d96148"}, "groups": "forest"}, "job": {"inputs": {"otu": {"src": "hda", "id": "7ce5ee5ae5d96148", "uuid": "629a26cb-120d-42bb-a917-3507c7a35418"}}, "update_time": "2018-02-08T17:48:11.584139", "tool_id": "mothur_list_otulabels", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "c77fbb66c7668cd4", "uuid": "e3a05278-a424-4f20-b031-29fa9a7fa9f8"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "717b2cf20a54ded4", "uuid": "4b2b6afc-25c4-4653-a862-79631562fb61"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "d2ce13293faca460", "uuid": "b6e06792-d467-48c8-b40b-51b038ab70ad"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "f0912769592a4e8c", "uuid": "e545aa5a-7692-42fb-b8d9-61ea22fe33a1"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "f0fe4746ca4a5cb1", "uuid": "dae9e7f3-2427-4449-90b8-17276da76712"}, "__new_primary_file_unique|0.16__": {"src": "hda", "id": "5828ffd76b6255d8", "uuid": "3a2848ec-f49a-49a7-bdea-50917937318c"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "13115f036dcfbd13", "uuid": "eddceaf9-34d4-4a66-b453-ad1e42fb8dc1"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "e10a735ff6c491f5", "uuid": "2d058ae9-31bd-49b6-94ac-77b47d0246ee"}, "__new_primary_file_unique|0.15__": {"src": "hda", "id": "09e374ba6c9df1b6", "uuid": "f90bc0fb-0b7e-44cf-b816-a72b1ed30834"}, "__new_primary_file_unique|0.08__": {"src": "hda", "id": "aa1c99020c7a5496", "uuid": "746158e2-fa91-4263-8728-7bfbce770538"}, "__new_primary_file_unique|0.14__": {"src": "hda", "id": "2ce508ad7dc7ffe8", "uuid": "2f412f03-52b6-4026-9667-a25b2be652be"}, "__new_primary_file_unique|0.13__": {"src": "hda", "id": "96df058c67bf3756", "uuid": "b6f88151-19b5-441e-b4a4-29ba406a55de"}, "__new_primary_file_unique|0.09__": {"src": "hda", "id": "1e1097535bca43f6", "uuid": "096f9562-7a76-42d3-ba5b-1d8004fbe29a"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "d9c53c113024c2ff", "uuid": "95f38409-54a2-458d-9c73-637d017ce72f"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "ae08f308b8be372c", "uuid": "644ef164-ef54-4991-b6e3-c14bf7306b09"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "b6c238a14dcfd0b8", "uuid": "33420052-8afa-4719-ac1c-c1821c4f9bf4"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "306338cd3056de25", "uuid": "3e5974d8-4c08-4504-b4b7-4b42af41f9a0"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "0ceb1b0e1e46c312", "uuid": "5a36fae3-2fa1-46f0-917f-76de86e29a70"}, "__new_primary_file_unique|0.25__": {"src": "hda", "id": "330f23492086f076", "uuid": "b22bb044-989b-495e-be17-366d614a309a"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "861415528bc25cb7", "uuid": "f6afa0f8-20e6-4d0a-9a1c-1ae169842bfc"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "938c47791fccd58a", "uuid": "d4f17b45-c40e-4a6c-94f8-b631ec5d925c"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "035ac92f40b8d8a9", "uuid": "0b125a96-5b32-4501-b360-b982ce27236e"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "2ba6ff9c01b5db74", "uuid": "b4acf26a-f6b5-40c6-b960-ecec9fe811b6"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "79c26bac844e1a03", "uuid": "637026ef-b3ed-4e17-b0f9-8ca825ee950d"}, "logfile": {"src": "hda", "id": "2df65164c2a87bdc", "uuid": "56e7ab14-244b-4ee0-b40e-6215c9c539fa"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "aa19462bf237ee74", "uuid": "cad5634f-3445-42ec-bb8f-ee3141eb3459"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "bd16ccfcb6f28f4b", "uuid": "2a3390f4-a79b-40e4-a074-06c1b585f817"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "8cada7d471147894", "uuid": "f0021787-d9ed-44fc-aeb7-e5ca738fa31f"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "4618478724b1d128", "uuid": "35b26fef-9160-4e42-bffc-7a9a2c2acd41"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "00a9b8f80d5c35db", "uuid": "9ff0b0f4-e24b-4a5b-a9ef-3c99aaa43615"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "e699037a579b0cad", "uuid": "298b1cee-f6b6-42fb-b5bd-bbb7b4057061"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "0f4cd4de4fddb960", "uuid": "ba0f8840-ec46-40dd-9346-2daf3d11a964"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "be56adfd92e0d058", "uuid": "f63c2a9e-b301-45a4-8689-b0dfe4216641"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "4502c5e78b18d95e", "uuid": "1b2321ce-5b3f-4ec2-aee6-5463412c94a3"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "710278472322a44f", "uuid": "57996085-931a-4897-87e3-a3ba1dc7a451"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "6a9e5657586fa330", "uuid": "218dd813-729e-4edb-a210-9efd78a05d10"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "5f438a17e0a96676", "uuid": "9c0a9e33-9cbd-4a88-8105-46a2d7a26145"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > list.otulabels(shared=otu.dat,groups=forest)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.otulabels\notu.0.01.otulabels\notu.0.02.otulabels\notu.0.03.otulabels\notu.0.04.otulabels\notu.0.05.otulabels\notu.0.06.otulabels\notu.0.07.otulabels\notu.0.08.otulabels\notu.0.09.otulabels\notu.0.10.otulabels\notu.0.11.otulabels\notu.0.12.otulabels\notu.0.13.otulabels\notu.0.14.otulabels\notu.0.15.otulabels\notu.0.16.otulabels\notu.0.17.otulabels\notu.0.18.otulabels\notu.0.19.otulabels\notu.0.20.otulabels\notu.0.21.otulabels\notu.0.22.otulabels\notu.0.23.otulabels\notu.0.24.otulabels\notu.0.25.otulabels\notu.0.26.otulabels\notu.0.27.otulabels\notu.0.29.otulabels\notu.0.32.otulabels\notu.0.33.otulabels\notu.0.36.otulabels\notu.0.38.otulabels\notu.0.41.otulabels\notu.0.45.otulabels\notu.0.55.otulabels\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1715.dat' otu.dat &&  echo 'list.otulabels( shared=otu.dat ,groups=forest )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:48:06.700381", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "\"forest\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24441", "id": "3a07e8fa101f66c3", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_list_otulabels.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"search|input": {"src": "hda", "id": "bddc530082ef8a20"}, "search|intype": "fasta"}, "job": {"inputs": {"input": {"src": "hda", "id": "bddc530082ef8a20", "uuid": "949ae96f-0362-4b67-92e8-be705e219275"}}, "update_time": "2018-02-08T17:48:30.417744", "tool_id": "mothur_list_seqs", "outputs": {"logfile": {"src": "hda", "id": "37b4fa647e89d65b", "uuid": "363b76a4-71ba-472d-b2af-a9993410eb84"}, "accnos": {"src": "hda", "id": "cc03cfa56ce85621", "uuid": "853392dc-4c63-478b-85cc-5f4a20fc9f9a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > list.seqs(fasta=search.input.dat)\n\nOutput File Names: \nsearch.input.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1753.dat' search.input.dat &&  echo 'list.seqs( fasta=search.input.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:48:27.251930", "params": {"search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 1753}]}, \"intype\": \"fasta\", \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24527", "id": "a8b7bad9a0464ba9", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_list_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"search|input": {"src": "hda", "id": "8fd9b8ef17ae00b1"}, "search|intype": "count"}, "job": {"inputs": {"input": {"src": "hda", "id": "8fd9b8ef17ae00b1", "uuid": "71a0a345-5ef4-451a-81d5-830ab3ad315c"}}, "update_time": "2018-02-08T17:48:47.846109", "tool_id": "mothur_list_seqs", "outputs": {"logfile": {"src": "hda", "id": "14a780cce250e27d", "uuid": "d3f0444f-4f52-44ad-ad38-44a9bca04a96"}, "accnos": {"src": "hda", "id": "812d58a31cb0e2dc", "uuid": "048efb02-e858-49f5-959c-8a122946fa2f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > list.seqs(count=search.input.dat)\n\nOutput File Names: \nsearch.input.accnos\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1756.dat' search.input.dat &&  echo 'list.seqs( count=search.input.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:48:44.763422", "params": {"search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 1756}]}, \"intype\": \"count\", \"__current_case__\": 7}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24617", "id": "7b32cfe10869d24e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_list_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "bfae85c1836289e5"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "bfae85c1836289e5", "uuid": "0f8f79f6-42d3-4908-9e5e-9fa7368630da"}}, "update_time": "2018-02-08T17:49:07.085680", "tool_id": "mothur_make_biom", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "0915854899960126", "uuid": "d64654a5-1a30-430a-ac1a-005c525a06b9"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "1b9599242429ea82", "uuid": "f55ce27e-c13d-493c-9d7f-c4444c538749"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "6a2c7b5090ae2641", "uuid": "2b0f00ed-c062-419e-929e-cb19c1e9cbc7"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "d8977dbfd5fe2600", "uuid": "016a6cad-0a69-4239-8e19-012adb3b3e06"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "1198cc8050ddcaae", "uuid": "6f6cae48-5375-443b-b28f-28d5ccfae448"}, "__new_primary_file_unique|0.16__": {"src": "hda", "id": "4b2729dfe19d84de", "uuid": "8319c5c2-6b30-48d4-86a9-6bcfe0da2c84"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "7027bb045e039323", "uuid": "62102e99-f3ec-4cee-bde5-baa2ef469b14"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "5608a3ee5cd775a6", "uuid": "5855cbdf-9ef8-4e03-9e39-6b08f909ad14"}, "__new_primary_file_unique|0.15__": {"src": "hda", "id": "fec153023f9b1d9e", "uuid": "77cb4dc6-b006-421b-a1de-07a50fc52ada"}, "__new_primary_file_unique|0.08__": {"src": "hda", "id": "003c8452d769ee89", "uuid": "8fc0f9e9-8437-48e0-97a4-48819ad9d079"}, "__new_primary_file_unique|0.14__": {"src": "hda", "id": "8163ea9a30f0397d", "uuid": "4661216f-bea5-40ce-ad43-7ec3be0de710"}, "__new_primary_file_unique|0.13__": {"src": "hda", "id": "8f46422d2f09daf7", "uuid": "2824087a-7d29-4de4-bc5b-1e5d570c097f"}, "__new_primary_file_unique|0.09__": {"src": "hda", "id": "a5a9105172fdd91a", "uuid": "c4b734f4-24d7-4db9-94d7-65c624345fb8"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "64eef14501ccd4ab", "uuid": "52662d8c-6207-41b7-b89e-efc9fb8ffd10"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "de02e3e208bf1269", "uuid": "c0b2f1ff-287f-42ff-91ac-b66d2c20b76c"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "e3f5b81c3cbfdcdf", "uuid": "4f669977-d70b-4bf9-ac7d-b151cd0519e9"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "11a4cfd609b30231", "uuid": "2a9fb9af-2e93-40c6-a070-1ddd29d71233"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "39f31be0d2a47263", "uuid": "c5860154-e79a-4168-92ad-b5cfa370c6c6"}, "__new_primary_file_unique|0.25__": {"src": "hda", "id": "167e0067a671882a", "uuid": "d9b9dc3d-f24e-413d-9435-02b84aadc3b0"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "d19d640fc3be2602", "uuid": "0e8f323c-3c29-4dfb-8da4-6e5256b824b9"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "1530f791843ef8a6", "uuid": "a0444193-49e6-4494-91c9-f54559c5b2dd"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "3dc5251947e7e28a", "uuid": "77a5052b-e9d0-427d-a791-6a87225a01cc"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "eb8ff02f919a6d53", "uuid": "63062340-9cb6-428d-a49a-8279ece828a5"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "0dc27fbedcc45ffc", "uuid": "de5d6db7-b33f-485b-939e-273ff9ec3430"}, "logfile": {"src": "hda", "id": "15a27f85b655084f", "uuid": "26755b2e-9832-4f7d-acb2-9d1d847c2b51"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "e14d9e71cf2baa46", "uuid": "4c3dd9a9-86f0-4518-ba22-e93881251f9d"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "aae81213b7398bbb", "uuid": "d0a16ace-ab73-4d26-93c3-0724b3887a6d"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "8730f173539a4bd2", "uuid": "b9342ef9-4afa-4a3e-a1c5-5175e0fe0da8"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "5bd80237c4b2a4d2", "uuid": "2ae4018d-6c82-40ea-a836-e45678ec92c7"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "3e009a540553e32f", "uuid": "52b0efc8-143b-49a5-94a7-9c0e0cf686ba"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "bd8570a9749b756e", "uuid": "2629c96b-cff5-4116-8545-b1349908a6c9"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "cfc1466e3cee5ffe", "uuid": "3ad83ef3-d941-4dfe-ba65-2faebc5c943e"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "90655b23123ebb49", "uuid": "06c79f68-a6b2-486b-9256-d2a202109b22"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "4df3a051f1ec097e", "uuid": "3c9f80b5-e238-47da-87b7-e809ad9650d2"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "5ac9d236a72d89c9", "uuid": "dc1a9140-6481-4007-80d2-082030ded364"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "71ecf7184a915076", "uuid": "c8c31def-b63e-4562-97d7-b33efb01d479"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "faecacf595ac39e2", "uuid": "2afa052a-b65f-4497-8a1d-a0ac9586133e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.biom(shared=otu.dat,matrixtype=sparse)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.biom\notu.0.01.biom\notu.0.02.biom\notu.0.03.biom\notu.0.04.biom\notu.0.05.biom\notu.0.06.biom\notu.0.07.biom\notu.0.08.biom\notu.0.09.biom\notu.0.10.biom\notu.0.11.biom\notu.0.12.biom\notu.0.13.biom\notu.0.14.biom\notu.0.15.biom\notu.0.16.biom\notu.0.17.biom\notu.0.18.biom\notu.0.19.biom\notu.0.20.biom\notu.0.21.biom\notu.0.22.biom\notu.0.23.biom\notu.0.24.biom\notu.0.25.biom\notu.0.26.biom\notu.0.27.biom\notu.0.29.biom\notu.0.32.biom\notu.0.33.biom\notu.0.36.biom\notu.0.38.biom\notu.0.41.biom\notu.0.45.biom\notu.0.55.biom\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1759.dat' otu.dat && ln -s 'None' constaxonomy.dat && ln -s 'None' metadata.dat &&  echo 'make.biom( shared=otu.dat, matrixtype=sparse )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:49:02.186797", "params": {"matrixtype": "\"sparse\"", "picrustc": "{\"use\": \"no\", \"__current_case__\": 1}", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "constaxonomy": "null", "metadata": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24703", "id": "3fc9b5ca07992501", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_biom.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "9f85b398b863e225"}, "groups": "forest", "label": ["0.36", "0.38", "0.41"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "9f85b398b863e225", "uuid": "60bfcab3-d3b9-44ff-aca3-32717277d27a"}}, "update_time": "2018-02-08T17:49:25.911998", "tool_id": "mothur_make_biom", "outputs": {"__new_primary_file_0.41|0.38__": {"src": "hda", "id": "6124a241728fed7b", "uuid": "b762f29a-2704-443f-b4d3-bbea479d086b"}, "logfile": {"src": "hda", "id": "101d321fbee7d3a2", "uuid": "83c2a1a4-92e5-4f94-83e5-cc2bb65c66bf"}, "__new_primary_file_0.41|0.36__": {"src": "hda", "id": "39279bb4f32c9cd5", "uuid": "0fef610e-5bb0-4a7f-90c3-a32bcb82e1cf"}, "__new_primary_file_0.41|0.41__": {"src": "hda", "id": "bcc6ea767bb5f894", "uuid": "8ad1e0bb-4ec2-4c11-8a8b-748de9043914"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.biom(shared=otu.dat,label=0.36-0.38-0.41,groups=forest,matrixtype= \rsparse)\n0.36\n0.38\n0.41\n\nOutput File Names: \notu.0.36.biom\notu.0.38.biom\notu.0.41.biom\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1797.dat' otu.dat && ln -s 'None' constaxonomy.dat && ln -s 'None' metadata.dat &&  echo 'make.biom( shared=otu.dat, label=0.36-0.38-0.41, groups=forest, matrixtype=sparse )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:49:22.733946", "params": {"matrixtype": "\"sparse\"", "picrustc": "{\"use\": \"no\", \"__current_case__\": 1}", "dbkey": "\"hg17\"", "label": "[\"0.36\", \"0.38\", \"0.41\"]", "groups": "\"forest\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "constaxonomy": "null", "metadata": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24791", "id": "6c12052addbdbf10", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_biom.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "45a7e4eec17b01cd"}, "constaxonomy": {"src": "hda", "id": "bf5dc6d85ce11a2a"}, "metadata": {"src": "hda", "id": "68fe6c8323c3e617"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "45a7e4eec17b01cd", "uuid": "c7c39dbf-9d32-4c75-aa2b-72d738c2356d"}, "constaxonomy": {"src": "hda", "id": "bf5dc6d85ce11a2a", "uuid": "2182557c-bb36-4e43-9f24-6026f34e8869"}, "metadata": {"src": "hda", "id": "68fe6c8323c3e617", "uuid": "b1eab905-87df-40e4-aaf2-697205e2c2ab"}}, "update_time": "2018-02-08T17:49:45.406914", "tool_id": "mothur_make_biom", "outputs": {"logfile": {"src": "hda", "id": "a54f199e2763d2d1", "uuid": "76e1e856-efb0-4095-9f38-8cb64dd2847e"}, "__new_primary_file_1|1__": {"src": "hda", "id": "7fc77adef3161147", "uuid": "56d5e4b4-b16b-44d9-9a30-7af0343c66cb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.biom(shared=otu.dat,constaxonomy=constaxonomy.dat,metadata=metadat \ra.dat,matrixtype=sparse)\n1\n\nOutput File Names: \notu.1.biom\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1802.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1803.dat' constaxonomy.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1804.dat' metadata.dat &&  echo 'make.biom( shared=otu.dat, constaxonomy=constaxonomy.dat, metadata=metadata.dat, matrixtype=sparse )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:49:42.311244", "params": {"matrixtype": "\"sparse\"", "picrustc": "{\"use\": \"no\", \"__current_case__\": 1}", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "24934", "id": "3cb3ad12c0574547", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_biom.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input_type|forward_fastq": {"src": "hda", "id": "40b793aeee43e4b6"}, "input_type|reverse_fastq": {"src": "hda", "id": "8da9ebed1ea03269"}, "input_type|type": "regular"}, "job": {"inputs": {"forward_fastq": {"src": "hda", "id": "40b793aeee43e4b6", "uuid": "d177e8df-000a-438c-866c-8da4fb15a7e8"}, "reverse_fastq": {"src": "hda", "id": "8da9ebed1ea03269", "uuid": "4183434a-6517-4bf4-8aef-45298a77e00e"}}, "update_time": "2018-02-08T17:50:06.290005", "tool_id": "mothur_make_contigs", "outputs": {"scrapqual": {"src": "hda", "id": "bb84ff5118ea4500", "uuid": "6a187a01-8e75-4077-aba6-27cf1b2efc0c"}, "scrapfasta": {"src": "hda", "id": "609fed3f705180b0", "uuid": "40ef29cd-1760-461e-837c-fb9cf9ef54fc"}, "qual": {"src": "hda", "id": "e106c55583a975c8", "uuid": "f8b1c8aa-4338-4084-9e20-156d7b490568"}, "report": {"src": "hda", "id": "9356319465a4ba53", "uuid": "1a949e57-40e4-4dfe-8baf-2eb21796226f"}, "fasta": {"src": "hda", "id": "a4b7a61fc28685f4", "uuid": "c618030d-ef87-4a9b-af99-137e62eaa53d"}, "logfile": {"src": "hda", "id": "67a1201bdc0a51a0", "uuid": "f83d1e2d-870d-42fe-9107-b5be8f0ddd26"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.contigs(ffastq=ffastq.dat,rfastq=rfastq.dat,align=needleman,match= \r1,mismatch=-1,gapopen=-2,gapextend=-1,processors=1)\n\nUsing 1 processors.\nMaking contigs...\n25\nDone.\nIt took 0 secs to process 25 sequences.\n\n\nOutput File Names: \nffastq.trim.contigs.fasta\nffastq.scrap.contigs.fasta\nffastq.trim.contigs.qual\nffastq.scrap.contigs.qual\nffastq.contigs.report\n\n[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1807.dat' ffastq.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1808.dat' rfastq.dat &&   echo 'make.contigs( ffastq=ffastq.dat, rfastq=rfastq.dat, align=needleman, match=1, mismatch=-1, gapopen=-2, gapextend=-1, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:50:02.824847", "params": {"oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "input_type": "{\"forward_fastq\": {\"values\": [{\"src\": \"hda\", \"id\": 1807}]}, \"reverse_fastq\": {\"values\": [{\"src\": \"hda\", \"id\": 1808}]}, \"type\": \"regular\", \"__current_case__\": 0}", "align": "\"needleman\"", "gapopen": "\"-2\"", "mismatch": "\"-1\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "gapextend": "\"-1\"", "match": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25043", "id": "032dc790b013bafc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_contigs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input_type|type": "simple_collection", "input_type|paired_collection": {"src": "hdca", "id": "b323ca264f40001e"}}, "job": {"inputs": {"paired_collection1": {"src": "hda", "id": "0e34f88fe3f1ff0f", "uuid": "c4b8cf08-3eaa-4a06-b0ce-2cfb892f5b33"}, "paired_collection2": {"src": "hda", "id": "f1d296c611fd20af", "uuid": "4980d4b2-7b82-452f-b610-85ef365a1cc6"}}, "update_time": "2018-02-08T17:50:39.239356", "tool_id": "mothur_make_contigs", "outputs": {"scrapqual": {"src": "hda", "id": "1c4bd19fb1ecc433", "uuid": "7b96413f-88d9-4095-8e81-41daaaf25b5b"}, "scrapfasta": {"src": "hda", "id": "5f1708e38b3558fc", "uuid": "50c50c4c-681f-4366-800b-0650b3179bcd"}, "qual": {"src": "hda", "id": "1bd9d366bb876da0", "uuid": "76592125-34b1-404a-bae8-e434bc0ecb57"}, "report": {"src": "hda", "id": "38241bcf61ff4dc4", "uuid": "e4407411-a51e-4918-be13-cae227dafa01"}, "fasta": {"src": "hda", "id": "0cf22b7aa65fb1a8", "uuid": "cec921c2-641b-47f7-b989-4a16060eb8bb"}, "logfile": {"src": "hda", "id": "2437f8b06af7836c", "uuid": "4998833e-6620-4888-8ebd-4427df633478"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.contigs(ffastq=ffastq.dat,rfastq=rfastq.dat,align=needleman,match= \r1,mismatch=-1,gapopen=-2,gapextend=-1,processors=1)\n\nUsing 1 processors.\nMaking contigs...\n25\nDone.\nIt took 0 secs to process 25 sequences.\n\n\nOutput File Names: \nffastq.trim.contigs.fasta\nffastq.scrap.contigs.fasta\nffastq.trim.contigs.qual\nffastq.scrap.contigs.qual\nffastq.contigs.report\n\n[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1815.dat' ffastq.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1816.dat' rfastq.dat &&   echo 'make.contigs( ffastq=ffastq.dat, rfastq=rfastq.dat, align=needleman, match=1, mismatch=-1, gapopen=-2, gapextend=-1, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:50:35.719002", "params": {"oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "input_type": "{\"paired_collection\": {\"values\": [{\"src\": \"hdca\", \"id\": 70}]}, \"type\": \"simple_collection\", \"__current_case__\": 1}", "align": "\"needleman\"", "gapopen": "\"-2\"", "mismatch": "\"-1\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "gapextend": "\"-1\"", "match": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25159", "id": "4a03c449ab1f345a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_contigs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input_type|type": "simple_collection", "input_type|paired_collection": {"src": "hdca", "id": "08fbf3fbfe908f7c"}, "align": "gotoh", "gapopen": "-3", "mismatch": "-2", "gapextend": "-2", "match": "2"}, "job": {"inputs": {"paired_collection1": {"src": "hda", "id": "91ae388b1da266fc", "uuid": "0b67f0e7-1839-4bf7-a7b6-7e9b43f66848"}, "paired_collection2": {"src": "hda", "id": "b97b38fe046d6cc3", "uuid": "86c5e085-9f4a-4f4c-9ae5-b8cfc143dd03"}}, "update_time": "2018-02-08T17:51:09.729195", "tool_id": "mothur_make_contigs", "outputs": {"scrapqual": {"src": "hda", "id": "d9efe2ab3f0b324f", "uuid": "b3333766-777b-4e7e-9ab5-93a62a99364f"}, "scrapfasta": {"src": "hda", "id": "8b7d704c8dec53b3", "uuid": "2ce03472-3cd8-484d-a1f2-740e8bd6573d"}, "qual": {"src": "hda", "id": "bd6616cdad8b15de", "uuid": "aa923b33-96f3-476e-8f3d-9c1698a89575"}, "report": {"src": "hda", "id": "9529b46206034a2c", "uuid": "ed4518c1-1549-4607-aa5d-0d416351c12c"}, "fasta": {"src": "hda", "id": "bde0ddf414dac721", "uuid": "04370737-4778-4385-9606-195aff41b2ac"}, "logfile": {"src": "hda", "id": "4c02de16bce2c9b2", "uuid": "7348bc0c-b9db-4660-81c0-f0822b689e9b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.contigs(ffastq=ffastq.dat,rfastq=rfastq.dat,align=gotoh,match=2,mi \rsmatch=-2,gapopen=-3,gapextend=-2,processors=1)\n\nUsing 1 processors.\nMaking contigs...\n25\nDone.\nIt took 1 secs to process 25 sequences.\n\n\nOutput File Names: \nffastq.trim.contigs.fasta\nffastq.scrap.contigs.fasta\nffastq.trim.contigs.qual\nffastq.scrap.contigs.qual\nffastq.contigs.report\n\n[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1823.dat' ffastq.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1824.dat' rfastq.dat &&   echo 'make.contigs( ffastq=ffastq.dat, rfastq=rfastq.dat, align=gotoh, match=2, mismatch=-2, gapopen=-3, gapextend=-2, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:51:06.412196", "params": {"oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "input_type": "{\"paired_collection\": {\"values\": [{\"src\": \"hdca\", \"id\": 71}]}, \"type\": \"simple_collection\", \"__current_case__\": 1}", "align": "\"gotoh\"", "gapopen": "\"-3\"", "mismatch": "\"-2\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "gapextend": "\"-2\"", "match": "\"2\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25275", "id": "2afa7a4578b8f4fd", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_contigs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input_type|type": "list_collection", "input_type|list_paired_collection": {"src": "hdca", "id": "ca4ebafec84c6506"}}, "job": {"inputs": {"list_paired_collection4": {"src": "hda", "id": "99e29abee4bbbed4", "uuid": "a78035ab-1253-4bb6-a4ca-3dc8352d355a"}, "list_paired_collection2": {"src": "hda", "id": "e655594793c63949", "uuid": "17cbba95-5854-4048-b01a-ae8523a58668"}, "list_paired_collection3": {"src": "hda", "id": "d5278219f70ebcfa", "uuid": "d2403292-9ed0-42fd-ae7c-07fee2f5166e"}, "list_paired_collection1": {"src": "hda", "id": "374d576ea0abb1c1", "uuid": "658855be-1bc8-4e8f-8016-92a344cb7f32"}}, "update_time": "2018-02-08T17:51:47.835378", "tool_id": "mothur_make_contigs", "outputs": {"scrapqual": {"src": "hda", "id": "6ccb9232700adf3a", "uuid": "e60c1270-4bfa-43d0-9b2c-5283f50341c8"}, "group": {"src": "hda", "id": "7843946a99274b74", "uuid": "bcc33c04-5751-496d-8025-9ffd9c43579b"}, "scrapfasta": {"src": "hda", "id": "6149d2026be5ab0e", "uuid": "3748da5e-abcc-4af1-9add-34059b824fb5"}, "qual": {"src": "hda", "id": "a5ab925c30b3f870", "uuid": "775aeca4-234d-449e-bdf2-f0313c2f18d3"}, "report": {"src": "hda", "id": "77ac7afdfe20d572", "uuid": "16a48568-2560-4d63-abf6-55dfa871ad94"}, "fasta": {"src": "hda", "id": "712f958ac1325a99", "uuid": "2c779df1-4ec7-466e-9fc5-c43a09076140"}, "logfile": {"src": "hda", "id": "7f39cb8d0fec48fe", "uuid": "f44c09a3-d08f-4a8c-9938-d7a117de4e71"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.contigs(file=combo_fastq.dat,align=needleman,match=1,mismatch=-1,g \rapopen=-2,gapextend=-1,processors=1)\n\nUsing 1 processors.\n\n>>>>>\tProcessing file pair dataset_1831.dat - dataset_1832.dat (files 1 of 2)\t<<<<<\nMaking contigs...\n25\nDone.\n\nIt took 0 secs to assemble 25 reads.\n\n\n>>>>>\tProcessing file pair dataset_1833.dat - dataset_1834.dat (files 2 of 2)\t<<<<<\nMaking contigs...\n5\nDone.\n\nIt took 0 secs to assemble 5 reads.\n\nIt took 0 secs to process 30 sequences.\n\nGroup count: \nPair1\t25\nPair2\t5\n\nTotal of all groups is 30\n\nOutput File Names: \ncombo_fastq.trim.contigs.fasta\ncombo_fastq.trim.contigs.qual\ncombo_fastq.contigs.report\ncombo_fastq.scrap.contigs.fasta\ncombo_fastq.scrap.contigs.qual\ncombo_fastq.contigs.groups\n\n[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s /tmp/saskia/tmpKSDp0p/files/001/dataset_1831.dat `basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1831.dat` && ln -s /tmp/saskia/tmpKSDp0p/files/001/dataset_1832.dat `basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1832.dat` && echo -e \"Pair1\\t`basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1831.dat`\\t`basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1832.dat`\" >> combo_fastq.dat && ln -s /tmp/saskia/tmpKSDp0p/files/001/dataset_1833.dat `basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1833.dat` && ln -s /tmp/saskia/tmpKSDp0p/files/001/dataset_1834.dat `basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1834.dat` && echo -e \"Pair2\\t`basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1833.dat`\\t`basename /tmp/saskia/tmpKSDp0p/files/001/dataset_1834.dat`\" >> combo_fastq.dat &&   echo 'make.contigs( file=combo_fastq.dat, align=needleman, match=1, mismatch=-1, gapopen=-2, gapextend=-1, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:51:43.455820", "params": {"oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "input_type": "{\"type\": \"list_collection\", \"list_paired_collection\": {\"values\": [{\"src\": \"hdca\", \"id\": 72}]}, \"__current_case__\": 2}", "align": "\"needleman\"", "gapopen": "\"-2\"", "mismatch": "\"-1\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "gapextend": "\"-1\"", "match": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25436", "id": "5c0379f640540f7d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_contigs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"groupings_0|name": "tardis", "source": {"src": "hda", "id": "c0114fb85356a3fb"}, "groupings_1|name": "dalek", "groupings_0|groups": ["forest", "pasture"], "groupings_1|groups": "pasture"}, "job": {"inputs": {"source": {"src": "hda", "id": "c0114fb85356a3fb", "uuid": "59f866f6-6861-4466-9249-f035d655cb8b"}}, "update_time": "2018-02-08T17:52:23.285242", "tool_id": "mothur_make_design", "outputs": {"design": {"src": "hda", "id": "7c99b6a4ddb58575", "uuid": "2039e3c1-2b85-4d57-a319-396e9b39b9b3"}}, "stdout": "", "command_line": "set -o pipefail;  echo -e \"forest\\ttardis\" >> /tmp/saskia/tmpKSDp0p/files/001/dataset_1843.dat; echo -e \"pasture\\ttardis\" >> /tmp/saskia/tmpKSDp0p/files/001/dataset_1843.dat; echo -e \"pasture\\tdalek\" >> /tmp/saskia/tmpKSDp0p/files/001/dataset_1843.dat;", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:52:20.357728", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groupings": "[{\"__index__\": 0, \"name\": \"tardis\", \"groups\": [\"forest\", \"pasture\"]}, {\"__index__\": 1, \"name\": \"dalek\", \"groups\": \"pasture\"}]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25542", "id": "2b215f192af96e2f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_design.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "4511ff07d3afd311"}, "qfile": {"src": "hda", "id": "ad82eee45b640977"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "4511ff07d3afd311", "uuid": "42033d28-15c3-43ee-8a75-a6338adcc78f"}, "qfile": {"src": "hda", "id": "ad82eee45b640977", "uuid": "b886b19e-0ebd-4723-b577-366f90f330eb"}}, "update_time": "2018-02-08T17:52:38.863124", "tool_id": "mothur_make_fastq", "outputs": {"fastq": {"src": "hda", "id": "41a06d54c9c9cb7c", "uuid": "ce1591c1-60c3-4e28-a73a-f8c98803cacd"}, "logfile": {"src": "hda", "id": "11da7bf4b3931f2a", "uuid": "057b847c-f6fe-4962-b476-b3b3cd574689"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.fastq(fasta=fasta.dat,qfile=qfile.dat)\n\nOutput File Names: \nfasta.fastq\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1844.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1845.dat' qfile.dat &&  echo 'make.fastq( fasta=fasta.dat, qfile=qfile.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:52:35.794214", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "chooseformat": "{\"use\": \"no\", \"__current_case__\": 1}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25644", "id": "ab313dd72b645b75", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_fastq.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "8e1caf8a5e3462d0"}, "chooseformat|use": "yes", "chooseformat|format": "illumina", "qfile": {"src": "hda", "id": "c6e05146e8b0a21e"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "8e1caf8a5e3462d0", "uuid": "e8632eb7-681b-4c70-898c-072215cc6faa"}, "qfile": {"src": "hda", "id": "c6e05146e8b0a21e", "uuid": "6eca077a-507f-4610-8455-e4bfecb1301c"}}, "update_time": "2018-02-08T17:52:59.564809", "tool_id": "mothur_make_fastq", "outputs": {"fastq": {"src": "hda", "id": "45c59e8d24947c4c", "uuid": "f306145c-649a-40d9-ba28-8f2bb5c8e5bf"}, "logfile": {"src": "hda", "id": "4855098d5a3d8633", "uuid": "a1bba381-c9dc-4f6f-95e4-bbe022811c74"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.fastq(fasta=fasta.dat,qfile=qfile.dat,format=illumina)\n\nOutput File Names: \nfasta.fastq\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1848.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1849.dat' qfile.dat &&  echo 'make.fastq( fasta=fasta.dat, qfile=qfile.dat ,format=illumina )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:52:56.419955", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "chooseformat": "{\"use\": \"yes\", \"__current_case__\": 0, \"format\": \"illumina\"}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25753", "id": "11fff4f70c354168", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_fastq.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"method|inputs_0|fasta": {"src": "hda", "id": "5690f3eca16a24c2"}, "method|inputs_1|group": "testgroup2", "method|inputs_0|group": "testgroup", "method|inputs_1|fasta": {"src": "hda", "id": "5690f3eca16a24c2"}, "method|how": "manually"}, "job": {"inputs": {"method|inputs_0|fasta": {"src": "hda", "id": "5690f3eca16a24c2", "uuid": "2e0c4243-034b-441f-b3b2-19e0a041de32"}, "method|inputs_1|fasta": {"src": "hda", "id": "5690f3eca16a24c2", "uuid": "2e0c4243-034b-441f-b3b2-19e0a041de32"}}, "update_time": "2018-02-08T17:53:21.184357", "tool_id": "mothur_make_group", "outputs": {"output": {"src": "hda", "id": "c2fd07bff4c5634d", "uuid": "c35e4cc0-bb7f-4b33-ad23-c8394419b96a"}, "logfile": {"src": "hda", "id": "3c09fc160c7c949a", "uuid": "8413a64d-b800-4ce9-9ef9-628ede96cdd6"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.group(fasta=fasta_0.dat-fasta_1.dat,groups=testgroup-testgroup2)\n\nOutput File Names: fasta_0.fasta_1.groups\n\n\nmothur > quit\n", "command_line": "set -o pipefail;   ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1853.dat' fasta_0.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1853.dat' fasta_1.dat &&  echo 'make.group( fasta=fasta_0.dat-fasta_1.dat, groups=testgroup-testgroup2 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:53:17.417101", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "{\"how\": \"manually\", \"__current_case__\": 1, \"inputs\": [{\"__index__\": 0, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 1853}]}, \"group\": \"testgroup\"}, {\"__index__\": 1, \"fasta\": {\"values\": [{\"src\": \"hda\", \"id\": 1853}]}, \"group\": \"testgroup2\"}]}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25879", "id": "cf6f5650773911ff", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_group.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"method|how": "collection", "method|fasta_collection": {"src": "hdca", "id": "b31f4d82ada5e956"}}, "job": {"inputs": {"fasta_collection2": {"src": "hda", "id": "ead8b19bd4100f06", "uuid": "9810929b-444b-47dd-aeb1-435bb19e9440"}, "fasta_collection1": {"src": "hda", "id": "ead8b19bd4100f06", "uuid": "9810929b-444b-47dd-aeb1-435bb19e9440"}}, "update_time": "2018-02-08T17:53:41.867928", "tool_id": "mothur_make_group", "outputs": {"output": {"src": "hda", "id": "1048ce0425f8cb59", "uuid": "11a01df2-365b-4ca7-8be2-27bc18e495c0"}, "logfile": {"src": "hda", "id": "8d7a576c822a8355", "uuid": "4b3ba1ce-f095-47d5-b798-fc7c8f5821d7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.group(fasta=fasta_testgroup.dat-fasta_testgroup2.dat,groups=testgr \roup-testgroup2)\n\nOutput File Names: fasta_testgroup.fasta_testgroup2.groups\n\n\nmothur > quit\n", "command_line": "set -o pipefail;   ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1857.dat' fasta_testgroup.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1857.dat' fasta_testgroup2.dat &&  echo 'make.group( fasta=fasta_testgroup.dat-fasta_testgroup2.dat, groups=testgroup-testgroup2 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:53:38.125674", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "{\"how\": \"collection\", \"fasta_collection\": {\"values\": [{\"src\": \"hdca\", \"id\": 73}]}, \"__current_case__\": 0}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "25990", "id": "6e055b0f6b730971", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_group.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "ecf48c02251dfb67"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "ecf48c02251dfb67", "uuid": "a1e67bd3-07a2-4356-a5c9-ddaf5aa4e700"}}, "update_time": "2018-02-08T17:53:56.373528", "tool_id": "mothur_make_lefse", "outputs": {"lefse_out": {"src": "hda", "id": "c30adaf179fc5aaa", "uuid": "02e1aead-76bc-4cc9-ba9e-9bcd1221ba6e"}, "logfile": {"src": "hda", "id": "388d1db82fb077e8", "uuid": "16207fbb-8b4a-4a67-8d62-dcf39553f42c"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.lefse(shared=otu.dat,scale=totalgroup)\nYou did not provide a label, I will use the first label in your inputfile.\n\nOutput File Names: \notu.unique.lefse\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1860.dat' otu.dat && ln -s 'None' design.dat && ln -s 'None' constaxonomy.dat &&  echo 'make.lefse( shared=otu.dat, scale=totalgroup )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:53:53.261854", "params": {"scale": "\"totalgroup\"", "dbkey": "\"hg17\"", "label": "null", "design": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "constaxonomy": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26077", "id": "cc61617d359bbeb4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_lefse.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"design": {"src": "hda", "id": "2472375c89218954"}, "otu": {"src": "hda", "id": "4f48e12496476004"}, "label": "0.18"}, "job": {"inputs": {"design": {"src": "hda", "id": "2472375c89218954", "uuid": "40876580-3afb-4f31-8f7b-bab66411eed3"}, "otu": {"src": "hda", "id": "4f48e12496476004", "uuid": "e90c477f-8e02-4657-84ab-4900b982a6fc"}}, "update_time": "2018-02-08T17:54:18.037929", "tool_id": "mothur_make_lefse", "outputs": {"lefse_out": {"src": "hda", "id": "a5002b1773fb3add", "uuid": "b145b155-24a6-4ed1-9769-8142168681db"}, "logfile": {"src": "hda", "id": "293a2e724ad85605", "uuid": "66059d43-b491-40a9-be2c-d4d1f7b5a047"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.lefse(relabund=otu.dat,design=design.dat,label=0.18,scale=totalgro \rup)\n\nOutput File Names: \notu.0.18.lefse\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1863.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1864.dat' design.dat && ln -s 'None' constaxonomy.dat &&  echo 'make.lefse( relabund=otu.dat, design=design.dat, label=0.18, scale=totalgroup )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:54:14.907485", "params": {"scale": "\"totalgroup\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "constaxonomy": "null", "dbkey": "\"hg17\"", "label": "\"0.18\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26188", "id": "8617c587cd9e4e77", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_lefse.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"reference|template": {"src": "hda", "id": "5383cf1b3b9fd9bd"}, "reference|source": "hist", "flow": {"src": "hda", "id": "dd4a25701e5bf03c"}, "error": {"src": "hda", "id": "ddb7b6e6b5a5748d"}}, "job": {"inputs": {"flow": {"src": "hda", "id": "dd4a25701e5bf03c", "uuid": "224fce87-9cc8-4912-bca5-c86096fedae9"}, "template": {"src": "hda", "id": "5383cf1b3b9fd9bd", "uuid": "60e32d13-d224-4951-89f2-827a0db4d984"}, "error": {"src": "hda", "id": "ddb7b6e6b5a5748d", "uuid": "05ddcf44-ecd1-45e4-989d-6ba2198d0fb5"}}, "update_time": "2018-02-08T17:54:42.911228", "tool_id": "mothur_make_lookup", "outputs": {"logfile": {"src": "hda", "id": "9695ced70a424d8b", "uuid": "0a0bb69d-b81a-4c73-988c-c32e3257d345"}, "lookup_out": {"src": "hda", "id": "7c234923b0122c52", "uuid": "e8efa2fc-1a1f-4ee8-acaf-f4a7f65a8999"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.lookup(reference=reference.template.dat,flow=flow.dat,error=error. \rdat,order=A,barcode=AACCGTGTC,key=TCAG,threshold=10000)\nGQY1XT001A8C6I != M00967_43_000000000-A3JHG_1_1101_11148_6457\nGQY1XT001BPRBN != M00967_43_000000000-A3JHG_1_1101_7079_6722\n\nData for homopolymer lengths of 0 and longer were imputed for this analysis\n\n\nOutput File Names: \nflow.lookup\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1867.dat' reference.template.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1868.dat' flow.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1869.dat' error.dat &&  echo 'make.lookup( reference=reference.template.dat, flow=flow.dat, error=error.dat, order=A, barcode=AACCGTGTC, key=TCAG, threshold=10000 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:54:39.698392", "params": {"reference": "{\"source\": \"hist\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 1867}]}, \"__current_case__\": 1}", "barcode": "\"AACCGTGTC\"", "dbkey": "\"hg17\"", "key": "\"TCAG\"", "threshold": "\"10000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "order": "\"A\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26384", "id": "fc6a9ef5f7630e87", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_lookup.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"reference|template": {"src": "hda", "id": "3989eef2a0b46a62"}, "barcode": "XAXAXCXCXGXTXGXTXC", "flow": {"src": "hda", "id": "af2e40921cfe1b21"}, "reference|source": "hist", "key": "XTXCXAXGX", "error": {"src": "hda", "id": "7a7dcacb06603266"}}, "job": {"inputs": {"flow": {"src": "hda", "id": "af2e40921cfe1b21", "uuid": "c96ef4ba-fb78-4d80-9013-40185fe043db"}, "template": {"src": "hda", "id": "3989eef2a0b46a62", "uuid": "01d49cac-26ff-4b61-82c2-6d0f8f04a9c0"}, "error": {"src": "hda", "id": "7a7dcacb06603266", "uuid": "a4fd69ea-45f1-4bbb-ab55-5e84c6aa4e30"}}, "update_time": "2018-02-08T17:55:06.797669", "tool_id": "mothur_make_lookup", "outputs": {"logfile": {"src": "hda", "id": "a2907571b551cae9", "uuid": "f842ac50-4067-4e7a-9e11-39cad5e7a7d7"}, "lookup_out": {"src": "hda", "id": "54704a1dcf64f2e8", "uuid": "7696d203-cf2b-46c7-b147-001e0dc86df5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.lookup(reference=reference.template.dat,flow=flow.dat,error=error. \rdat,order=A,barcode=AACCGTGTC,key=TCAG,threshold=10000)\nGQY1XT001A8C6I != M00967_43_000000000-A3JHG_1_1101_11148_6457\nGQY1XT001BPRBN != M00967_43_000000000-A3JHG_1_1101_7079_6722\n\nData for homopolymer lengths of 0 and longer were imputed for this analysis\n\n\nOutput File Names: \nflow.lookup\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1872.dat' reference.template.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1873.dat' flow.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1874.dat' error.dat &&  echo 'make.lookup( reference=reference.template.dat, flow=flow.dat, error=error.dat, order=A, barcode=AACCGTGTC, key=TCAG, threshold=10000 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:55:03.580091", "params": {"reference": "{\"source\": \"hist\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 1872}]}, \"__current_case__\": 1}", "barcode": "\"XAXAXCXCXGXTXGXTXC\"", "dbkey": "\"hg17\"", "key": "\"XTXCXAXGX\"", "threshold": "\"10000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "order": "\"A\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26513", "id": "dd28ab0e62f6c657", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_lookup.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"intype|infile": "biom", "intype|otu": {"src": "hda", "id": "9f7864eb5fec163b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "9f7864eb5fec163b", "uuid": "dd47f7cd-9004-4ed5-bd85-1c25d74c261c"}}, "update_time": "2018-02-08T17:55:24.413838", "tool_id": "mothur_make_shared", "outputs": {"shared": {"src": "hda", "id": "fd1c56392329a112", "uuid": "6784c2f8-881c-4339-84f6-d79007188b0b"}, "logfile": {"src": "hda", "id": "f78fa183df45cc17", "uuid": "90f3f7f2-1148-4fae-b6eb-3be63593972a"}, "groupout": {"src": "hda", "id": "e6696f8460301cd8", "uuid": "bb629e4d-c6ee-4f53-bb9c-a82ca1454555"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.shared(biom=intype_otu.dat)\n\nuserLabel\n\nOutput File Names: \nintype_otu.shared\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1877.dat' intype_otu.dat &&  echo 'make.shared( biom=intype_otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log &&  mv mothur.*.logfile \"/tmp/saskia/tmpKSDp0p/files/001/dataset_1878.dat\" && mv intype_otu*.shared \"/tmp/saskia/tmpKSDp0p/files/001/dataset_1879.dat\"", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:55:21.200554", "params": {"intype": "{\"infile\": \"biom\", \"__current_case__\": 1, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1877}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26602", "id": "4dfde39352bb574f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"intype|infile": "otulist", "intype|group": {"src": "hda", "id": "7f99cfb1de31b6f4"}, "intype|otu": {"src": "hda", "id": "d4490cd22d2e91a2"}}, "job": {"inputs": {"group": {"src": "hda", "id": "7f99cfb1de31b6f4", "uuid": "6d5585d0-a1f5-46f0-b357-325d6b02b5a2"}, "otu": {"src": "hda", "id": "d4490cd22d2e91a2", "uuid": "b85240a3-aaec-45f8-bf25-008930ce7ae9"}}, "update_time": "2018-02-08T17:55:45.993342", "tool_id": "mothur_make_shared", "outputs": {"shared": {"src": "hda", "id": "7967c060fcc2b0c3", "uuid": "65a75bf7-90f6-45d6-8be1-01d3a2cb6092"}, "logfile": {"src": "hda", "id": "d911dc399b1b3959", "uuid": "ae0a8ddf-438e-4ca9-b113-5bf60e2578b1"}, "groupout": {"src": "hda", "id": "a6619ad3bbdc2f3d", "uuid": "83193b9b-370e-4845-b426-943fc8a35c9f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.shared(group=intype_group.dat,list=intype_otu.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \nintype_otu.shared\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1881.dat' intype_otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1882.dat' intype_group.dat &&  echo 'make.shared( group=intype_group.dat, list=intype_otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log &&  mv mothur.*.logfile \"/tmp/saskia/tmpKSDp0p/files/001/dataset_1883.dat\" && mv intype_otu*.shared \"/tmp/saskia/tmpKSDp0p/files/001/dataset_1884.dat\"", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:55:42.150192", "params": {"intype": "{\"group\": {\"values\": [{\"src\": \"hda\", \"id\": 1882}]}, \"__current_case__\": 0, \"label\": null, \"groups\": null, \"infile\": \"otulist\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1881}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26721", "id": "f060dd6bec0b0c91", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"intype|infile": "otulist", "intype|group": {"src": "hda", "id": "11cbcf7169f85c4f"}, "intype|otu": {"src": "hda", "id": "3ac08cc66e07c165"}, "intype|groups": ["forest", "pasture"], "intype|label": ["0.03", "0.05", "0.22"]}, "job": {"inputs": {"group": {"src": "hda", "id": "11cbcf7169f85c4f", "uuid": "24f0a7f3-acf4-48e6-a19b-701ae5977f5b"}, "otu": {"src": "hda", "id": "3ac08cc66e07c165", "uuid": "b2fb6d6f-d5c1-4e8c-ba17-afa3ccf9791a"}}, "update_time": "2018-02-08T17:56:10.243068", "tool_id": "mothur_make_shared", "outputs": {"groupout": {"src": "hda", "id": "ca3baaede20d3608", "uuid": "187fa39c-3715-445d-b050-6e8e9df82e58"}, "__new_primary_file_0.22|0.22__": {"src": "hda", "id": "65fc46f73aabdfda", "uuid": "4d84238e-343f-48a4-9a0d-6ba323b6bbf8"}, "__new_primary_file_0.22|0.05__": {"src": "hda", "id": "16eec28fa6281f7f", "uuid": "5652e0e4-810d-45e7-8ea9-fb1a38d404d8"}, "shared": {"src": "hda", "id": "1bab9e4fed59ebfb", "uuid": "4dd2c469-e1db-4a00-b840-1e880cd3e460"}, "logfile": {"src": "hda", "id": "0d9db12bc460aef9", "uuid": "42cb6d93-e1a3-40a6-a678-c6c1c4d5d9b3"}, "__new_primary_file_0.22|0.03__": {"src": "hda", "id": "b042b0cfab22e670", "uuid": "6843b9dc-09d3-4a7c-b42e-ecbc82632993"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.shared(group=intype_group.dat,label=0.03-0.05-0.22,groups=forest-p \rasture,list=intype_otu.dat)\n0.03\n0.05\n0.22\n\nOutput File Names: \nintype_otu.forest.pasture.groups\nintype_otu.0.03.shared\nintype_otu.0.05.shared\nintype_otu.0.22.shared\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1886.dat' intype_otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1887.dat' intype_group.dat &&  echo 'make.shared( group=intype_group.dat, label=0.03-0.05-0.22, groups=forest-pasture, list=intype_otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log &&  mv mothur.*.logfile \"/tmp/saskia/tmpKSDp0p/files/001/dataset_1888.dat\" && mv intype_otu*.groups \"/tmp/saskia/tmpKSDp0p/files/001/dataset_1890.dat\"", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:56:06.575770", "params": {"intype": "{\"group\": {\"values\": [{\"src\": \"hda\", \"id\": 1887}]}, \"__current_case__\": 0, \"label\": [\"0.03\", \"0.05\", \"0.22\"], \"groups\": [\"forest\", \"pasture\"], \"infile\": \"otulist\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 1886}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/488/galaxy_488.sh: line 40: [: too many arguments\n", "job_metrics": [], "model_class": "Job", "external_id": "26831", "id": "d13b0aeade1f3b9f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_shared.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"project": {"src": "hda", "id": "55d802277995b0ed"}, "sff": {"src": "hda", "id": "9adfeb8ffc5068e4"}, "mimark": {"src": "hda", "id": "6124c38139ecb629"}, "oligos": {"src": "hda", "id": "14500b6333a1070c"}}, "job": {"inputs": {"project": {"src": "hda", "id": "55d802277995b0ed", "uuid": "bac32361-557f-42dc-8ca5-4cb8c17348a9"}, "oligos": {"src": "hda", "id": "14500b6333a1070c", "uuid": "a25517e0-bfdc-4afe-a916-8caaafb04375"}, "sff": {"src": "hda", "id": "9adfeb8ffc5068e4", "uuid": "4051a32d-cd21-4c47-b718-55969c1da954"}, "mimark": {"src": "hda", "id": "6124c38139ecb629", "uuid": "704c7182-88d1-43e6-a8dc-7133cba88d86"}}, "update_time": "2018-02-08T17:56:46.294658", "tool_id": "mothur_make_sra", "outputs": {"submission_xml": {"src": "hda", "id": "4f9964cac71ceae2", "uuid": "25e41557-5ee7-452d-8456-eea7543d75c7"}, "flow_out": {"src": "hda", "id": "a625551c8e7496b4", "uuid": "8e7b6655-e359-470c-9fc3-4e101bbf3b67"}, "qual_out": {"src": "hda", "id": "0d7bfb86ba13c2bf", "uuid": "3505c479-7e32-4834-aa0d-fd4583bfa61b"}, "fasta_out": {"src": "hda", "id": "269645e76dd38019", "uuid": "fa9e3c7a-4f42-4d4e-a835-df97df662e48"}, "scrap_sff": {"src": "hda", "id": "4f070c1374b9df0b", "uuid": "7b4ae88a-44a5-46c6-9bdc-118a5aa48166"}, "logfile": {"src": "hda", "id": "6d9db605bb466f8a", "uuid": "c25b3e9e-1b70-4be5-9b9f-eaeaf6c32309"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > make.sra(project=project.dat,sff=sff.dat,oligos=oligos.dat,mimark=mimar \rk.dat,bdiffs=0,pdiffs=0,tdiffs=0,ldiffs=0,sdiffs=0,checkorient=false,orientation \r=forward,platform=_LS454,instrument=454_GS,libstrategy=AMPLICON,libselection=PCR \r,libsource=METAGENOMIC,datatype=METAGENOME,trim=True,includescrap=True)\n\n/******************************************/\nRunning command: sffinfo(sff=sff.dat, oligos=oligos.dat, trim=True)\nExtracting info from sff.dat ...\n10\nIt took 0 secs to extract 10.\n\nOutput File Names: \nsff.fasta\nsff.qual\nsff.flow\nsff.scrap.sff\n\n/******************************************/\n\nOutput File Names: \nsff.fasta\nsff.qual\nsff.flow\nsff.scrap.sff\nsubmission.xml\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1894.dat' project.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1895.dat' sff.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1896.dat' oligos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1897.dat' mimark.dat && ln -s 'None' fastq.dat &&  echo 'make.sra( project=project.dat, sff=sff.dat, oligos=oligos.dat, mimark=mimark.dat, bdiffs=0, pdiffs=0, tdiffs=0, ldiffs=0, sdiffs=0, checkorient=false, orientation=forward, platform=_LS454, instrument=454_GS, libstrategy=AMPLICON, libselection=PCR, libsource=METAGENOMIC, datatype=METAGENOME, trim=True, includescrap=True )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:56:41.999131", "params": {"bdiffs": "\"0\"", "trim": "\"true\"", "sdiffs": "\"0\"", "libselection": "\"PCR\"", "ldiffs": "\"0\"", "libsource": "\"METAGENOMIC\"", "checkorient": "\"false\"", "fastq": "null", "pdiffs": "\"0\"", "dbkey": "\"hg17\"", "includescrap": "\"true\"", "instrument": "\"454_GS\"", "datatype": "\"METAGENOME\"", "orientation": "\"forward\"", "platform": "\"_LS454\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "libstrategy": "\"AMPLICON\"", "tdiffs": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "26993", "id": "4c17a0c0b24f3d2a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_make_sra.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"dist": {"src": "hda", "id": "72ec7f16ae254bf0"}, "dist2": {"src": "hda", "id": "96c8304a26dfa89d"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "72ec7f16ae254bf0", "uuid": "69e3357c-572a-4248-ba48-1ae412fb9be5"}, "dist2": {"src": "hda", "id": "96c8304a26dfa89d", "uuid": "a043bab0-8e7d-4047-9d55-f3184fba1218"}}, "update_time": "2018-02-08T17:57:29.492577", "tool_id": "mothur_mantel", "outputs": {"logfile": {"src": "hda", "id": "0750df27179eb44a", "uuid": "0c3d1424-d5a6-4a69-b0fb-e01c603c2749"}, "mantel": {"src": "hda", "id": "a0d6fe44ad497cef", "uuid": "42af4d39-71bc-4850-90d1-5986cfc8e4a5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > mantel(phylip1=dist.dat,phylip2=dist2.dat,method=pearson,iters=1000)\n\nmantel = 0.304745\tpValue = 0.000000\n\nOutput File Names: \ndist.mantel\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1904.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1905.dat' dist2.dat &&  echo 'mantel( phylip1=dist.dat, phylip2=dist2.dat, method=pearson, iters=1000 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:57:26.139913", "params": {"iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"pearson\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27140", "id": "2c905c266975a822", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_mantel.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"merge|type": "fasta", "merge|inputs": [{"src": "hda", "id": "de3e1eb0e9cadbab"}, {"src": "hda", "id": "417510e0ae171d2e"}, {"src": "hda", "id": "6e2b9e3a5eac2ec6"}]}, "job": {"inputs": {"inputs2": {"src": "hda", "id": "417510e0ae171d2e", "uuid": "9467c807-a9f3-4740-8c68-3ff70ccdcc9f"}, "inputs": {"src": "hda", "id": "de3e1eb0e9cadbab", "uuid": "0de05468-1a0f-4cf1-b8af-474e0cc3cf31"}, "inputs1": {"src": "hda", "id": "de3e1eb0e9cadbab", "uuid": "0de05468-1a0f-4cf1-b8af-474e0cc3cf31"}, "inputs3": {"src": "hda", "id": "6e2b9e3a5eac2ec6", "uuid": "354c013c-439a-4dcb-87a8-f5716c2cfec2"}}, "update_time": "2018-02-08T17:57:56.177705", "tool_id": "mothur_merge_files", "outputs": {"output": {"src": "hda", "id": "0fb2e145d63428e3", "uuid": "d1a7062b-9bce-4396-a7b8-2a276cefc398"}, "logfile": {"src": "hda", "id": "b8e3f2c4e0441645", "uuid": "88fa2ee1-a971-4a14-9fde-78c8e4124b17"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.files(input=input0.dat-input1.dat-input2.dat,output=/tmp/saskia/t \rmpKSDp0p/files/001/dataset_1912.dat)\n\nOutput File Names: \n/tmp/saskia/tmpKSDp0p/files/001/dataset_1912.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1908.dat' input0.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1909.dat' input1.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1910.dat' input2.dat &&  echo 'merge.files( input=input0.dat-input1.dat-input2.dat-, output=/tmp/saskia/tmpKSDp0p/files/001/dataset_1912.dat )' | sed 's/ //g' | sed 's/-,/,/g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:57:53.020816", "params": {"merge": "{\"inputs\": {\"values\": [{\"src\": \"hda\", \"id\": 1908}, {\"src\": \"hda\", \"id\": 1909}, {\"src\": \"hda\", \"id\": 1910}]}, \"type\": \"fasta\", \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27277", "id": "5932136d963c1318", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_files.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"design|source": "hist", "design|design_dataset": {"src": "hda", "id": "32a578a19336cfbe"}, "otu": {"src": "hda", "id": "78f9790ceb9e760a"}}, "job": {"inputs": {"design_dataset": {"src": "hda", "id": "32a578a19336cfbe", "uuid": "53411ffe-5c48-4de5-914e-2143f57be4fe"}, "otu": {"src": "hda", "id": "78f9790ceb9e760a", "uuid": "b01887a3-f0fe-408f-9ae7-e2a382c4c9f9"}}, "update_time": "2018-02-08T17:58:17.037551", "tool_id": "mothur_merge_groups", "outputs": {"merged_shared": {"src": "hda", "id": "46591abe7f08ccf9", "uuid": "036b9366-aeeb-4334-b1bc-28eba7afbf33"}, "logfile": {"src": "hda", "id": "b0f3daede2de0400", "uuid": "1f85c9aa-1a03-4684-96e1-6bc38e54b5ed"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.groups(design=design_dataset.dat,shared=otu.dat,method=sum)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.merge.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1913.dat' otu.dat && ln -s 'None' group.dat && ln -s 'None' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1914.dat' design_dataset.dat &&  echo 'merge.groups( design=design_dataset.dat ,shared=otu.dat ,method=sum )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:58:13.874471", "params": {"group": "null", "dbkey": "\"hg17\"", "label": "null", "design": "{\"source\": \"hist\", \"design_dataset\": {\"values\": [{\"src\": \"hda\", \"id\": 1914}]}, \"__current_case__\": 0}", "groups": "null", "fasta": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"sum\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27386", "id": "b7c449f860774475", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_groups.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"design|source": "hist", "design|design_dataset": {"src": "hda", "id": "41e5dce11cc91f7a"}, "otu": {"src": "hda", "id": "d36489c18c908bb1"}, "groups": ["forest", "pasture"], "label": ["0.05", "0.22", "0.38"]}, "job": {"inputs": {"design_dataset": {"src": "hda", "id": "41e5dce11cc91f7a", "uuid": "587ebff1-49e7-47f6-bd51-d7b2e4b3521a"}, "otu": {"src": "hda", "id": "d36489c18c908bb1", "uuid": "23cfb8bb-56fa-4193-84db-7d4adf3f91f1"}}, "update_time": "2018-02-08T17:58:38.787975", "tool_id": "mothur_merge_groups", "outputs": {"merged_shared": {"src": "hda", "id": "ab07adc211b2df50", "uuid": "bf4c1384-c484-4f17-a982-c58fbd809afd"}, "logfile": {"src": "hda", "id": "6b8aa44b4322962a", "uuid": "c5f34277-320d-489a-9e08-74a73979c558"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.groups(design=design_dataset.dat,shared=otu.dat,groups=forest-pas \rture,label=0.05-0.22-0.38,method=sum)\n0.05\n0.22\n0.38\n\nOutput File Names: \notu.merge.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1917.dat' otu.dat && ln -s 'None' group.dat && ln -s 'None' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1918.dat' design_dataset.dat &&  echo 'merge.groups( design=design_dataset.dat ,shared=otu.dat ,groups=forest-pasture ,label=0.05-0.22-0.38 ,method=sum )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:58:35.565687", "params": {"group": "null", "dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.22\", \"0.38\"]", "design": "{\"source\": \"hist\", \"design_dataset\": {\"values\": [{\"src\": \"hda\", \"id\": 1918}]}, \"__current_case__\": 0}", "groups": "[\"forest\", \"pasture\"]", "fasta": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"sum\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27513", "id": "5300091d026f85af", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_groups.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"design|design_dataset": {"src": "hda", "id": "e4b594eefb7aada3"}, "design|source": "hist", "group": {"src": "hda", "id": "b81396351716a7ed"}}, "job": {"inputs": {"group": {"src": "hda", "id": "b81396351716a7ed", "uuid": "3b9b1091-7209-4254-88c3-d8ade7e87586"}, "design_dataset": {"src": "hda", "id": "e4b594eefb7aada3", "uuid": "9cb733df-b949-4852-ac5b-76459cd4cdac"}}, "update_time": "2018-02-08T17:58:59.407641", "tool_id": "mothur_merge_groups", "outputs": {"merged_group": {"src": "hda", "id": "58a81f0c48a42115", "uuid": "a1a56d3a-ac4a-4557-96a8-201b4e48ecd8"}, "logfile": {"src": "hda", "id": "d7ea930ce32eed6a", "uuid": "f3c9e925-f54a-4def-99c8-724daed3eeda"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.groups(design=design_dataset.dat,group=group.dat,method=sum)\n\nOutput File Names: \ngroup.merge.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s 'None' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1921.dat' group.dat && ln -s 'None' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1922.dat' design_dataset.dat &&  echo 'merge.groups( design=design_dataset.dat ,group=group.dat ,method=sum )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:58:56.393115", "params": {"dbkey": "\"hg17\"", "label": "null", "design": "{\"source\": \"hist\", \"design_dataset\": {\"values\": [{\"src\": \"hda\", \"id\": 1922}]}, \"__current_case__\": 0}", "groups": "null", "fasta": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"sum\"", "otu": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27627", "id": "3808e741d551ae79", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_groups.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"design|design_dataset": {"src": "hda", "id": "7e1cf2195f01e827"}, "fasta": {"src": "hda", "id": "8f85c19787d8d333"}, "design|source": "hist", "method": "median", "group": {"src": "hda", "id": "983faa3420093487"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "8f85c19787d8d333", "uuid": "621a07be-1a42-4c72-9e04-2f089737f369"}, "group": {"src": "hda", "id": "983faa3420093487", "uuid": "e36ee2d6-ce27-4d5d-ab87-3b6dea9473de"}, "design_dataset": {"src": "hda", "id": "7e1cf2195f01e827", "uuid": "7f20534c-ce2e-4dde-985b-6fbf6eaff13b"}}, "update_time": "2018-02-08T17:59:24.175570", "tool_id": "mothur_merge_groups", "outputs": {"merged_group": {"src": "hda", "id": "930b92102bb55843", "uuid": "821f7ea2-87d4-4404-a237-0e409f05737c"}, "logfile": {"src": "hda", "id": "c8e74883aba54288", "uuid": "8c385a77-3e61-47d5-89a0-0c42618d1bcc"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.groups(design=design_dataset.dat,count=group.dat,fasta=fasta.dat, \rmethod=median)\n\nOutput File Names: \ngroup.merge.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s 'None' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1925.dat' group.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1926.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1927.dat' design_dataset.dat &&  echo 'merge.groups( design=design_dataset.dat ,count=group.dat ,fasta=fasta.dat ,method=median )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:59:20.306073", "params": {"dbkey": "\"hg17\"", "label": "null", "design": "{\"source\": \"hist\", \"design_dataset\": {\"values\": [{\"src\": \"hda\", \"id\": 1927}]}, \"__current_case__\": 0}", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"median\"", "otu": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27759", "id": "966d85c09a3ba224", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_groups.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"design|groupings_1|groups": "pasture", "otu": {"src": "hda", "id": "f4fa0c7fbb0e3e2c"}, "design|groupings_1|name": "dalek", "design|source": "build", "design|groupings_0|name": "tardis", "design|groupings_0|groups": "forest"}, "job": {"inputs": {"otu": {"src": "hda", "id": "f4fa0c7fbb0e3e2c", "uuid": "bf95dd8a-844f-44de-948f-c2a3f12be527"}}, "update_time": "2018-02-08T17:59:43.854854", "tool_id": "mothur_merge_groups", "outputs": {"merged_shared": {"src": "hda", "id": "531aa3b82ca54fa4", "uuid": "ae812da7-ca13-425d-b496-10763dd23c3c"}, "logfile": {"src": "hda", "id": "d6bfe7e8caebca0c", "uuid": "797514f7-25de-4561-876c-0419c3f03080"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.groups(design=generated_design.dat,shared=otu.dat,method=sum)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.merge.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1930.dat' otu.dat && ln -s 'None' group.dat && ln -s 'None' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/job_working_directory/000/515/tmpqonpbe' generated_design.dat &&  echo 'merge.groups( design=generated_design.dat ,shared=otu.dat ,method=sum )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T17:59:40.668151", "params": {"group": "null", "dbkey": "\"hg17\"", "label": "null", "design": "{\"source\": \"build\", \"__current_case__\": 1, \"groupings\": [{\"__index__\": 0, \"name\": \"tardis\", \"groups\": \"forest\"}, {\"__index__\": 1, \"name\": \"dalek\", \"groups\": \"pasture\"}]}", "groups": "null", "fasta": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"sum\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27855", "id": "499ab5633737b2d3", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_groups.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"input": [{"src": "hda", "id": "ebca6ff66bc47ca1"}, {"src": "hda", "id": "a3e90b92a8eb33dd"}]}, "job": {"inputs": {"input2": {"src": "hda", "id": "a3e90b92a8eb33dd", "uuid": "3a88c872-f075-41ba-88e3-1918baa76798"}, "input": {"src": "hda", "id": "ebca6ff66bc47ca1", "uuid": "8adc62cb-4747-49d1-b76a-2d67dab4f20b"}, "input1": {"src": "hda", "id": "ebca6ff66bc47ca1", "uuid": "8adc62cb-4747-49d1-b76a-2d67dab4f20b"}}, "update_time": "2018-02-08T18:00:05.520447", "tool_id": "mothur_merge_sfffiles", "outputs": {"output": {"src": "hda", "id": "2c072c8536d83576", "uuid": "954a0bc5-6d95-4df0-a108-937947278295"}, "logfile": {"src": "hda", "id": "cfb1f8928a5313e1", "uuid": "ab073c04-3281-4dbe-9c2e-4e9f798c9477"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.sfffiles(sff=input0.dat-input1.dat,output=/tmp/saskia/tmpKSDp0p/f \riles/001/dataset_1936.dat)\n\nMerging info from input0.dat ...\n10\nIt took 0 secs to merge 10.\n\nMerging info from input1.dat ...\n10\nIt took 0 secs to merge 10.\n\nOutput File Names: \n/tmp/saskia/tmpKSDp0p/files/001/dataset_1936.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1933.dat' input0.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1934.dat' input1.dat &&  echo 'merge.sfffiles( sff=input0.dat-input1.dat-, output=/tmp/saskia/tmpKSDp0p/files/001/dataset_1936.dat )' | sed 's/ //g' | sed 's/-,/,/g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:00:02.377604", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "27963", "id": "93ee5b88b9257311", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_sfffiles.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input": [{"src": "hda", "id": "b0e21127fa89f6b7"}, {"src": "hda", "id": "d5b0791da63d7742"}]}, "job": {"inputs": {"input2": {"src": "hda", "id": "d5b0791da63d7742", "uuid": "d24e9354-aa59-4ca3-9534-d33059c79a3a"}, "input": {"src": "hda", "id": "b0e21127fa89f6b7", "uuid": "45c7f81e-3ec8-42db-a7cf-7843326d2ef2"}, "input1": {"src": "hda", "id": "b0e21127fa89f6b7", "uuid": "45c7f81e-3ec8-42db-a7cf-7843326d2ef2"}}, "update_time": "2018-02-08T18:00:27.242056", "tool_id": "mothur_merge_taxsummary", "outputs": {"output": {"src": "hda", "id": "0a1e7528e524af83", "uuid": "d4525a7a-178e-49f0-b2b7-832a173efeeb"}, "logfile": {"src": "hda", "id": "d8247bdcb1ad4f59", "uuid": "01051fd2-1cdf-4514-9f3f-a46f8633c19b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > merge.taxsummary(input=input0.dat-input1.dat,output=/tmp/saskia/tmpKSDp \r0p/files/001/dataset_1940.dat)\n\nOutput File Names: \n/tmp/saskia/tmpKSDp0p/files/001/dataset_1940.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1937.dat' input0.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1938.dat' input1.dat &&  echo 'merge.taxsummary( input=input0.dat-input1.dat-, output=/tmp/saskia/tmpKSDp0p/files/001/dataset_1940.dat )' | sed 's/ //g' | sed 's/-,/,/g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:00:24.083311", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28083", "id": "17228a24cf52bb1d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_merge_taxsummary.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"design": {"src": "hda", "id": "ccfc4e50dfc4db8c"}, "otu": {"src": "hda", "id": "5c8c831e231041b4"}}, "job": {"inputs": {"design": {"src": "hda", "id": "ccfc4e50dfc4db8c", "uuid": "0856f7dd-c311-4b6a-b610-c3e61e131c2d"}, "otu": {"src": "hda", "id": "5c8c831e231041b4", "uuid": "98c0269c-613d-4f6b-945b-b03e15c2eef8"}}, "update_time": "2018-02-08T18:00:49.964815", "tool_id": "mothur_metastats", "outputs": {"__new_primary_file_unique.tardis_dalek|0.25.tardis_dalek__": {"src": "hda", "id": "23edcc4e5b71eb61", "uuid": "e254a57d-6b92-485b-94b2-696a0f583f48"}, "__new_primary_file_unique.tardis_dalek|0.10.tardis_dalek__": {"src": "hda", "id": "6488c2c82f28f195", "uuid": "9d4229d8-efcf-49eb-8a99-7db53404486c"}, "__new_primary_file_unique.tardis_dalek|unique.tardis_dalek__": {"src": "hda", "id": "d5d307ba80698737", "uuid": "323b9c27-cfd3-4404-b148-460f4ae42f08"}, "__new_primary_file_unique.tardis_dalek|0.14.tardis_dalek__": {"src": "hda", "id": "0dd59bf0ff2d1808", "uuid": "dfe825b4-560d-46a6-a3fe-0ac86cc953f2"}, "__new_primary_file_unique.tardis_dalek|0.08.tardis_dalek__": {"src": "hda", "id": "8a43e709b6288a8e", "uuid": "7a35cb2e-6457-415a-b628-7c6428c66950"}, "__new_primary_file_unique.tardis_dalek|0.16.tardis_dalek__": {"src": "hda", "id": "e6e401f2a6b47613", "uuid": "e1a05933-bbad-4222-8b53-7677210586ab"}, "__new_primary_file_unique.tardis_dalek|0.17.tardis_dalek__": {"src": "hda", "id": "b1038f71a0d34df9", "uuid": "8e37a662-e02b-4176-a95b-fabfbd1b54c0"}, "__new_primary_file_unique.tardis_dalek|0.05.tardis_dalek__": {"src": "hda", "id": "89a6b602b1c79537", "uuid": "25ef581d-b984-4e1a-86e3-92a5c09ff2ea"}, "__new_primary_file_unique.tardis_dalek|0.13.tardis_dalek__": {"src": "hda", "id": "be88353ca733c0a1", "uuid": "f887bb42-5613-4c7f-b8ce-1a7e359f4d86"}, "__new_primary_file_unique.tardis_dalek|0.15.tardis_dalek__": {"src": "hda", "id": "6aa2efcb07ffa2aa", "uuid": "1c0e7350-e2a9-409a-9d75-f567ad255b0c"}, "__new_primary_file_unique.tardis_dalek|0.11.tardis_dalek__": {"src": "hda", "id": "b033e717893f975b", "uuid": "4af371eb-6d68-4208-b8a7-963d774c3d81"}, "__new_primary_file_unique.tardis_dalek|0.12.tardis_dalek__": {"src": "hda", "id": "c81b3d5aeaa214d9", "uuid": "0db9589f-a364-4371-8181-877bd52bdaca"}, "__new_primary_file_unique.tardis_dalek|0.32.tardis_dalek__": {"src": "hda", "id": "f438c8126c9bf9b0", "uuid": "1d1e9de4-e49b-4959-9b7b-cbd46afa9329"}, "__new_primary_file_unique.tardis_dalek|0.29.tardis_dalek__": {"src": "hda", "id": "f44604ff22d877c1", "uuid": "1899c047-5d53-4daa-86dd-d17c5916e643"}, "__new_primary_file_unique.tardis_dalek|0.07.tardis_dalek__": {"src": "hda", "id": "128c838a8d0d8ae0", "uuid": "97c67190-a01f-41cf-bedc-4dd3961ff510"}, "__new_primary_file_unique.tardis_dalek|0.04.tardis_dalek__": {"src": "hda", "id": "f3e6c274e0f9a8e4", "uuid": "2dc69c47-4aae-4a5e-ab1e-30b1373dc644"}, "__new_primary_file_unique.tardis_dalek|0.36.tardis_dalek__": {"src": "hda", "id": "03e89c7d01c2bc89", "uuid": "6b97a604-d0a5-448d-a089-ab2b10bc01a8"}, "__new_primary_file_unique.tardis_dalek|0.06.tardis_dalek__": {"src": "hda", "id": "976e02c1336449e2", "uuid": "04f6416e-10fa-42d7-af71-fd9beb5985fb"}, "__new_primary_file_unique.tardis_dalek|0.03.tardis_dalek__": {"src": "hda", "id": "26c4db6085811fea", "uuid": "4929f085-b59f-4194-bc17-1383398f70b3"}, "__new_primary_file_unique.tardis_dalek|0.09.tardis_dalek__": {"src": "hda", "id": "4981d0805809f979", "uuid": "8a11f0ad-8c4c-4d12-97e4-6bd9d22581c1"}, "__new_primary_file_unique.tardis_dalek|0.18.tardis_dalek__": {"src": "hda", "id": "81eed33b79c62dd6", "uuid": "fe2f8394-859e-4a4b-9ebe-4372133e3df7"}, "__new_primary_file_unique.tardis_dalek|0.01.tardis_dalek__": {"src": "hda", "id": "c17cb498f643f865", "uuid": "bbfb19a1-2947-41ab-b79d-db72dad84646"}, "__new_primary_file_unique.tardis_dalek|0.19.tardis_dalek__": {"src": "hda", "id": "e0803aa76a0a1bc2", "uuid": "afdb1fec-9dde-461d-ad0e-6a5ae28017fa"}, "__new_primary_file_unique.tardis_dalek|0.23.tardis_dalek__": {"src": "hda", "id": "5a2b531ed34953ef", "uuid": "cf779b61-a8ea-4883-87f5-c91c3e292dd9"}, "__new_primary_file_unique.tardis_dalek|0.55.tardis_dalek__": {"src": "hda", "id": "d275e0f086e8ba53", "uuid": "f5572494-b2a1-467c-a450-59d5ddee16c6"}, "__new_primary_file_unique.tardis_dalek|0.41.tardis_dalek__": {"src": "hda", "id": "a30e41ecd967d7a3", "uuid": "210829b9-80c0-465c-a757-f398c22b056a"}, "__new_primary_file_unique.tardis_dalek|0.38.tardis_dalek__": {"src": "hda", "id": "a93799b0b587d22c", "uuid": "a233d11b-6442-4375-ac8e-0fd1a4352846"}, "__new_primary_file_unique.tardis_dalek|0.22.tardis_dalek__": {"src": "hda", "id": "3eb471ae316d5ad9", "uuid": "f392ddea-025a-4c4d-8edf-a40147cb5a79"}, "__new_primary_file_unique.tardis_dalek|0.26.tardis_dalek__": {"src": "hda", "id": "c37b0acee3e6ddf8", "uuid": "a8c15b1f-1e11-4233-9f2f-4b151ac8cce6"}, "__new_primary_file_unique.tardis_dalek|0.33.tardis_dalek__": {"src": "hda", "id": "97255621df457a9d", "uuid": "9c76e42d-2704-4ca7-bc5e-941fc0640f2c"}, "__new_primary_file_unique.tardis_dalek|0.20.tardis_dalek__": {"src": "hda", "id": "f8c8bf4b82d11e77", "uuid": "4c8e26a6-19dd-44d6-812c-99d1043ee603"}, "__new_primary_file_unique.tardis_dalek|0.24.tardis_dalek__": {"src": "hda", "id": "19a2bc99dc38847c", "uuid": "1a182621-41c5-45e6-84b5-3c37158ba384"}, "__new_primary_file_unique.tardis_dalek|0.27.tardis_dalek__": {"src": "hda", "id": "7cddf8abc6fb76de", "uuid": "29a51c5e-589a-41e9-b6d3-cf95d9255dfc"}, "__new_primary_file_unique.tardis_dalek|0.21.tardis_dalek__": {"src": "hda", "id": "0bb6efe930f641f6", "uuid": "86a71f87-c4d6-493e-b5a1-09e26728f8a9"}, "logfile": {"src": "hda", "id": "21321643249e498c", "uuid": "b00f8c3e-8a53-4d25-b87d-906fd2778752"}, "__new_primary_file_unique.tardis_dalek|0.45.tardis_dalek__": {"src": "hda", "id": "8ecc395ead7daa5b", "uuid": "52cf9561-ba5e-4430-ba24-776b1fd17c80"}, "__new_primary_file_unique.tardis_dalek|0.02.tardis_dalek__": {"src": "hda", "id": "fe80aaa5fa3c02fc", "uuid": "60280cc1-03f0-4df8-9587-8cd48eeb6f91"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > metastats(shared=otu.dat,design=design.dat,iters=1000,threshold=0.05,pr \rocessors=1)\n\nUsing 1 processors.\nunique\nComparing tardis and dalek...\n\n\n\n0.01\nComparing tardis and dalek...\n\n\n\n0.02\nComparing tardis and dalek...\n\n\n\n0.03\nComparing tardis and dalek...\n\n\n\n0.04\nComparing tardis and dalek...\n\n\n\n0.05\nComparing tardis and dalek...\n\n\n\n0.06\nComparing tardis and dalek...\n\n\n\n0.07\nComparing tardis and dalek...\n\n\n\n0.08\nComparing tardis and dalek...\n\n\n\n0.09\nComparing tardis and dalek...\n\n\n\n0.10\nComparing tardis and dalek...\n\n\n\n0.11\nComparing tardis and dalek...\n\n\n\n0.12\nComparing tardis and dalek...\n\n\n\n0.13\nComparing tardis and dalek...\n\n\n\n0.14\nComparing tardis and dalek...\n\n\n\n0.15\nComparing tardis and dalek...\n\n\n\n0.16\nComparing tardis and dalek...\n\n\n\n0.17\nComparing tardis and dalek...\n\n\n\n0.18\nComparing tardis and dalek...\n\n\n\n0.19\nComparing tardis and dalek...\n\n\n\n0.20\nComparing tardis and dalek...\n\n\n\n0.21\nComparing tardis and dalek...\n\n\n\n0.22\nComparing tardis and dalek...\n\n\n\n0.23\nComparing tardis and dalek...\n\n\n\n0.24\nComparing tardis and dalek...\n\n\n\n0.25\nComparing tardis and dalek...\n\n\n\n0.26\nComparing tardis and dalek...\n\n\n\n0.27\nComparing tardis and dalek...\n\n\n\n0.29\nComparing tardis and dalek...\n\n\n\n0.32\nComparing tardis and dalek...\n\n\n\n0.33\nComparing tardis and dalek...\n\n\n\n0.36\nComparing tardis and dalek...\n\n\n\n0.38\nComparing tardis and dalek...\n\n\n\n0.41\nComparing tardis and dalek...\n\n\n\n0.45\nComparing tardis and dalek...\n\n\n\n0.55\nComparing tardis and dalek...\n\n\n\n\nOutput File Names: \notu.unique.tardis_dalek.metastats\notu.0.01.tardis_dalek.metastats\notu.0.02.tardis_dalek.metastats\notu.0.03.tardis_dalek.metastats\notu.0.04.tardis_dalek.metastats\notu.0.05.tardis_dalek.metastats\notu.0.06.tardis_dalek.metastats\notu.0.07.tardis_dalek.metastats\notu.0.08.tardis_dalek.metastats\notu.0.09.tardis_dalek.metastats\notu.0.10.tardis_dalek.metastats\notu.0.11.tardis_dalek.metastats\notu.0.12.tardis_dalek.metastats\notu.0.13.tardis_dalek.metastats\notu.0.14.tardis_dalek.metastats\notu.0.15.tardis_dalek.metastats\notu.0.16.tardis_dalek.metastats\notu.0.17.tardis_dalek.metastats\notu.0.18.tardis_dalek.metastats\notu.0.19.tardis_dalek.metastats\notu.0.20.tardis_dalek.metastats\notu.0.21.tardis_dalek.metastats\notu.0.22.tardis_dalek.metastats\notu.0.23.tardis_dalek.metastats\notu.0.24.tardis_dalek.metastats\notu.0.25.tardis_dalek.metastats\notu.0.26.tardis_dalek.metastats\notu.0.27.tardis_dalek.metastats\notu.0.29.tardis_dalek.metastats\notu.0.32.tardis_dalek.metastats\notu.0.33.tardis_dalek.metastats\notu.0.36.tardis_dalek.metastats\notu.0.38.tardis_dalek.metastats\notu.0.41.tardis_dalek.metastats\notu.0.45.tardis_dalek.metastats\notu.0.55.tardis_dalek.metastats\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1941.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1942.dat' design.dat &&  echo 'metastats( shared=otu.dat, design=design.dat, iters=1000, threshold=0.05, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:00:44.770100", "params": {"iters": "\"1000\"", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "sets": "null", "threshold": "\"0.05\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28202", "id": "9c170123467f3230", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_metastats.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"iters": "42", "label": ["0.03", "0.05", "0.23"], "design": {"src": "hda", "id": "f5f83a2c2e2df452"}, "groups": ["forest", "pasture"], "sets": ["tardis", "dalek"], "threshold": "0.1", "otu": {"src": "hda", "id": "16015188b50ec89d"}}, "job": {"inputs": {"design": {"src": "hda", "id": "f5f83a2c2e2df452", "uuid": "b2bfb765-b8ed-45fb-8868-718771a6b982"}, "otu": {"src": "hda", "id": "16015188b50ec89d", "uuid": "ee5a9e25-e463-4fe6-94ca-fec5c0b46ae0"}}, "update_time": "2018-02-08T18:01:12.674158", "tool_id": "mothur_metastats", "outputs": {"__new_primary_file_0.23.tardis_dalek|0.03.tardis_dalek__": {"src": "hda", "id": "d300bc462cc13705", "uuid": "f876c2bb-7428-4ce4-81b8-3088bff3409f"}, "logfile": {"src": "hda", "id": "1f58a7ab4f77b22a", "uuid": "8984636b-b45c-4592-a0ee-afce3170e0c5"}, "__new_primary_file_0.23.tardis_dalek|0.23.tardis_dalek__": {"src": "hda", "id": "e03f21306103e4ea", "uuid": "f048a2fc-77e9-41ce-99bb-40045453e1e2"}, "__new_primary_file_0.23.tardis_dalek|0.05.tardis_dalek__": {"src": "hda", "id": "262c1246e01f8d26", "uuid": "47ee5a3d-772d-401e-b3e3-de1424399d36"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > metastats(shared=otu.dat,design=design.dat,label=0.03-0.05-0.23,groups= \rforest-pasture,sets=tardis-dalek,iters=42,threshold=0.1,processors=1)\n\nUsing 1 processors.\n0.03\nComparing tardis and dalek...\n\n\n\n0.05\nComparing tardis and dalek...\n\n\n\n0.23\nComparing tardis and dalek...\n\n\n\n\nOutput File Names: \notu.0.03.tardis_dalek.metastats\notu.0.05.tardis_dalek.metastats\notu.0.23.tardis_dalek.metastats\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1980.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1981.dat' design.dat &&  echo 'metastats( shared=otu.dat, design=design.dat, label=0.03-0.05-0.23, groups=forest-pasture, sets=tardis-dalek, iters=42, threshold=0.1, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:01:09.437646", "params": {"iters": "\"42\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.23\"]", "groups": "[\"forest\", \"pasture\"]", "sets": "[\"tardis\", \"dalek\"]", "threshold": "\"0.1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28310", "id": "c9376b9862484ed4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_metastats.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"biosample_in": {"src": "hda", "id": "783b5c0953b1d59f"}}, "job": {"inputs": {"biosample_in": {"src": "hda", "id": "783b5c0953b1d59f", "uuid": "f04d010f-490e-47d7-9c58-638de0a0f112"}}, "update_time": "2018-02-08T18:01:30.104939", "tool_id": "mothur_mimarks_attributes", "outputs": {"logfile": {"src": "hda", "id": "7fc2bbf196a6c236", "uuid": "380bef89-2a78-4c3e-874a-739dcb8e6b44"}, "source_out": {"src": "hda", "id": "484bc14fb0641f5d", "uuid": "5f2c33dd-8ec2-49ef-8273-f4070a612f4b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > mimarks.attributes(xml=biosample_in.dat)\n\nOutput File Names: \nbiosample_in.source\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1986.dat' biosample_in.dat &&  echo 'mimarks.attributes( xml=biosample_in.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:01:27.084739", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28401", "id": "a15361ef356dda4c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_mimarks_attributes.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"maxiters": "500", "dist": {"src": "hda", "id": "b5c63bdc9af8cbfc"}, "iters": "10", "epsilon": "1e-12", "axes": {"src": "hda", "id": "79c845a60c77ee0a"}, "mindim": "1", "maxdim": "2"}, "job": {"inputs": {"axes": {"src": "hda", "id": "79c845a60c77ee0a", "uuid": "daa0cf22-d069-4512-92c4-00ccec312827"}, "dist": {"src": "hda", "id": "b5c63bdc9af8cbfc", "uuid": "a5bd2d21-a2d7-4102-877c-fd2380c0f335"}}, "update_time": "2018-02-08T18:01:52.474808", "tool_id": "mothur_nmds", "outputs": {"nmds_axes": {"src": "hda", "id": "fb839e143095d9fa", "uuid": "081a3528-a9b7-4eaa-a884-7ff38c3a8191"}, "logfile": {"src": "hda", "id": "69390d7537a983f9", "uuid": "154d81fb-90af-4c69-82af-c808c507e7ae"}, "nmds_stress": {"src": "hda", "id": "ad8f0faec2def4cc", "uuid": "2323c312-fef4-440b-957e-a17723a6996e"}, "nmds_iters": {"src": "hda", "id": "d227a40fd9141984", "uuid": "2f3b4e0e-a3ce-41e0-8619-22f3456e16bf"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > nmds(phylip=dist.dat,axes=axes.dat,mindim=1,maxdim=2,iters=10,maxiters= \r500,epsilon=0.000000000001)\nProcessing Dimension: 1\n1\n2\n3\n4\n5\n6\n7\n8\n9\n10\nProcessing Dimension: 2\n1\n2\n3\n4\n5\n6\n7\n8\n9\n10\n\nNumber of dimensions:\t2\nLowest stress :\t0.291989\nR-squared for configuration:\t0.672714\n\nOutput File Names: \ndist.nmds.iters\ndist.nmds.stress\ndist.nmds.axes\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1989.dat' dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1990.dat' axes.dat &&  echo 'nmds( phylip=dist.dat ,axes=axes.dat ,mindim=1 ,maxdim=2 ,iters=10 ,maxiters=500  ,epsilon=0.000000000001 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:01:48.716400", "params": {"iters": "\"10\"", "epsilon": "\"1e-12\"", "maxiters": "\"500\"", "dbkey": "\"hg17\"", "mindim": "\"1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "maxdim": "\"2\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28517", "id": "9cb939e9f07d29cd", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_nmds.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "48c25e118b57ff38"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "48c25e118b57ff38", "uuid": "8a3f167d-d835-41c1-a038-18adbb58214e"}}, "update_time": "2018-02-08T18:02:08.863250", "tool_id": "mothur_normalize_shared", "outputs": {"__new_primary_file_unique.norm|0.07.norm__": {"src": "hda", "id": "7759c88734df315e", "uuid": "a75f4462-3a2f-4cc2-b859-9a340492b5a7"}, "__new_primary_file_unique.norm|0.19.norm__": {"src": "hda", "id": "e15558a60db6ce87", "uuid": "05f65c04-ef5e-4021-b38c-b24d1edabb41"}, "__new_primary_file_unique.norm|0.21.norm__": {"src": "hda", "id": "49f819ba53a576ae", "uuid": "287b454e-235d-448d-beb9-72c57e385e9f"}, "__new_primary_file_unique.norm|0.27.norm__": {"src": "hda", "id": "272369349a8921ab", "uuid": "c50e231d-00fb-4c12-aacd-2c55c6aed2b1"}, "__new_primary_file_unique.norm|0.02.norm__": {"src": "hda", "id": "c2d6d1dec01a4ef9", "uuid": "d5787ed8-9289-4c0d-8654-4559c8b67bd4"}, "__new_primary_file_unique.norm|0.10.norm__": {"src": "hda", "id": "90fe3cef3e1f3d0a", "uuid": "0dce828e-85e6-4778-9f4d-a737f5bf061d"}, "__new_primary_file_unique.norm|0.15.norm__": {"src": "hda", "id": "cfc3a68225d7a57a", "uuid": "fe6355f9-4e84-4c08-941d-f686872e9fa9"}, "__new_primary_file_unique.norm|0.32.norm__": {"src": "hda", "id": "3a39b817c56902e0", "uuid": "c50f8300-a0e6-4171-a176-b7b7eded04cc"}, "__new_primary_file_unique.norm|0.17.norm__": {"src": "hda", "id": "2f054c8ffebf41aa", "uuid": "5accca94-4b16-42d9-9947-ef9a7e2ffb6e"}, "__new_primary_file_unique.norm|0.16.norm__": {"src": "hda", "id": "46333212c23a3768", "uuid": "b5d1bda0-7373-413b-acbf-eeb5146961e2"}, "__new_primary_file_unique.norm|0.36.norm__": {"src": "hda", "id": "75cd1d05bb846784", "uuid": "77ba217e-f20f-474f-94f3-5f21264485f4"}, "__new_primary_file_unique.norm|0.18.norm__": {"src": "hda", "id": "b87b913e52a5d5c9", "uuid": "74191fb6-286c-44ee-a8f1-2ed5bdbdf1e9"}, "__new_primary_file_unique.norm|0.09.norm__": {"src": "hda", "id": "27e1efdc333ce8f0", "uuid": "8d783925-c7e6-447e-8cc7-6d3b3bfb94ec"}, "__new_primary_file_unique.norm|0.13.norm__": {"src": "hda", "id": "2d594f1751c3f1ca", "uuid": "9ba75684-ca69-4ab3-ac4a-e03abe56de6d"}, "__new_primary_file_unique.norm|0.04.norm__": {"src": "hda", "id": "1e9ece54ea08d532", "uuid": "3647f93e-adbb-46b8-be78-b4dd866a3c1a"}, "__new_primary_file_unique.norm|0.25.norm__": {"src": "hda", "id": "2c56b3e8d1933dff", "uuid": "bd5cb805-5151-4fa8-b6ad-04cd367774ec"}, "__new_primary_file_unique.norm|0.08.norm__": {"src": "hda", "id": "d1c342b47833ac58", "uuid": "01a00306-6ea4-4f89-af13-fecec911d3d0"}, "__new_primary_file_unique.norm|0.14.norm__": {"src": "hda", "id": "3c42490c0523ccef", "uuid": "77eda36d-e783-4d80-98b1-a478e6b72e29"}, "__new_primary_file_unique.norm|0.01.norm__": {"src": "hda", "id": "c824299315999632", "uuid": "fd126526-1c4c-40a5-aa68-bd3ab81d043d"}, "__new_primary_file_unique.norm|0.12.norm__": {"src": "hda", "id": "a47b8bff4e8d501d", "uuid": "3043e307-5930-4373-a1cf-d0b4f8652103"}, "__new_primary_file_unique.norm|0.20.norm__": {"src": "hda", "id": "73da0ed5a2fb6fff", "uuid": "a68dd3f4-94f3-4214-b2aa-885b42bad8e3"}, "__new_primary_file_unique.norm|0.11.norm__": {"src": "hda", "id": "40b29ef9311f652c", "uuid": "5a54bdc9-f200-46fd-bcda-65cc9a198ddb"}, "__new_primary_file_unique.norm|0.24.norm__": {"src": "hda", "id": "b54047d5cce3c175", "uuid": "046417cb-59f0-49bb-b84e-217d6f9fc6df"}, "__new_primary_file_unique.norm|0.33.norm__": {"src": "hda", "id": "36c9940fe6749118", "uuid": "facb3a3c-29f8-4b19-91eb-7f9d9cebb1eb"}, "__new_primary_file_unique.norm|0.06.norm__": {"src": "hda", "id": "81ad05cab5ca23e3", "uuid": "52ee6aff-4754-400d-871e-b63c5a579dac"}, "logfile": {"src": "hda", "id": "f6fa49db00a5d176", "uuid": "49c3d551-24d6-4177-aa4d-f30a2ed85679"}, "__new_primary_file_unique.norm|0.22.norm__": {"src": "hda", "id": "3d07c4b2ea0d3aa3", "uuid": "fd2adbbe-a2a9-46ed-b5e3-d851f5d8c826"}, "__new_primary_file_unique.norm|0.23.norm__": {"src": "hda", "id": "8d52c605ebf1b6c9", "uuid": "0c921b87-30c0-49c6-8055-863f572a2d44"}, "__new_primary_file_unique.norm|unique.norm__": {"src": "hda", "id": "60c77f9904c7dacb", "uuid": "4f1c6b3b-c49e-4cde-9bcf-bc3b9b24bf92"}, "__new_primary_file_unique.norm|0.55.norm__": {"src": "hda", "id": "ecbc034f3494529a", "uuid": "f5274456-1f23-4cb1-8d2a-8a283213cd9a"}, "__new_primary_file_unique.norm|0.29.norm__": {"src": "hda", "id": "977623ec5ac25552", "uuid": "49ca3d12-5f9b-43d5-99d2-bc253f076536"}, "__new_primary_file_unique.norm|0.05.norm__": {"src": "hda", "id": "43b804562da00ba8", "uuid": "6ef2e7b3-cbad-4fa8-b8ac-ef215b7a04ba"}, "__new_primary_file_unique.norm|0.41.norm__": {"src": "hda", "id": "eeea002e11b8cacd", "uuid": "b683fd5c-efcc-49d6-8bd8-005ee6c05de2"}, "__new_primary_file_unique.norm|0.45.norm__": {"src": "hda", "id": "eceb0fa9b153422c", "uuid": "82f45968-c33c-4374-a80e-58acd43b3a5f"}, "__new_primary_file_unique.norm|0.26.norm__": {"src": "hda", "id": "a9b1685bdd21a57d", "uuid": "e8ec4d17-2204-45d2-901b-7763a9eb00c6"}, "__new_primary_file_unique.norm|0.38.norm__": {"src": "hda", "id": "85d4d338e8b329c0", "uuid": "2be1bc01-fadd-4ae6-ae51-fc2fa9b83bb6"}, "__new_primary_file_unique.norm|0.03.norm__": {"src": "hda", "id": "ae1816dcf1be843e", "uuid": "5d23b3c7-215f-4720-ac0c-8fce664b4c0d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > normalize.shared(shared=otu.dat,makerelabund=false,method=totalgroup)\nNormalizing to 49.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.norm.shared\notu.0.01.norm.shared\notu.0.02.norm.shared\notu.0.03.norm.shared\notu.0.04.norm.shared\notu.0.05.norm.shared\notu.0.06.norm.shared\notu.0.07.norm.shared\notu.0.08.norm.shared\notu.0.09.norm.shared\notu.0.10.norm.shared\notu.0.11.norm.shared\notu.0.12.norm.shared\notu.0.13.norm.shared\notu.0.14.norm.shared\notu.0.15.norm.shared\notu.0.16.norm.shared\notu.0.17.norm.shared\notu.0.18.norm.shared\notu.0.19.norm.shared\notu.0.20.norm.shared\notu.0.21.norm.shared\notu.0.22.norm.shared\notu.0.23.norm.shared\notu.0.24.norm.shared\notu.0.25.norm.shared\notu.0.26.norm.shared\notu.0.27.norm.shared\notu.0.29.norm.shared\notu.0.32.norm.shared\notu.0.33.norm.shared\notu.0.36.norm.shared\notu.0.38.norm.shared\notu.0.41.norm.shared\notu.0.45.norm.shared\notu.0.55.norm.shared\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/001/dataset_1995.dat' otu.dat &&  echo 'normalize.shared( shared=otu.dat, makerelabund=false ,method=totalgroup )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:02:04.195701", "params": {"makerelabund": "\"false\"", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"totalgroup\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28605", "id": "9c51eb665ea2103a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_normalize_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "9ba5a8797c4d0c42"}, "method": "zscore", "groups": ["forest", "pasture"], "label": ["0.03", "0.05", "0.22", "0.26"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "9ba5a8797c4d0c42", "uuid": "a4a49ce3-1b9f-49ae-aa48-ea0fc8e7daa7"}}, "update_time": "2018-02-08T18:02:27.725869", "tool_id": "mothur_normalize_shared", "outputs": {"__new_primary_file_0.26.norm|0.22.norm__": {"src": "hda", "id": "657c12bf3606453d", "uuid": "29a1882d-2c27-4382-8da0-48f9a2b9d275"}, "__new_primary_file_0.26.norm|0.03.norm__": {"src": "hda", "id": "0cced470bd87c555", "uuid": "6c7a4cab-4a52-4632-a961-fd87ee7abfe5"}, "logfile": {"src": "hda", "id": "d13e42b04e9821cb", "uuid": "7b373694-be5e-4685-a6a5-a70069e6c927"}, "__new_primary_file_0.26.norm|0.05.norm__": {"src": "hda", "id": "e58fc15b0924c233", "uuid": "3afbd0b9-3417-4574-a7c2-f5d92de0c7c2"}, "__new_primary_file_0.26.norm|0.26.norm__": {"src": "hda", "id": "4b63a0979ffefabe", "uuid": "084e8dac-f27e-40d4-a25a-2f528d29542f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > normalize.shared(relabund=otu.dat,label=0.03-0.05-0.22-0.26,groups=fore \rst-pasture,method=zscore)\n0.03\n0.05\n0.22\n0.26\n\nOutput File Names: \notu.0.03.norm.shared\notu.0.05.norm.shared\notu.0.22.norm.shared\notu.0.26.norm.shared\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2033.dat' otu.dat &&  echo 'normalize.shared( relabund=otu.dat ,label=0.03-0.05-0.22-0.26 ,groups=forest-pasture ,method=zscore )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:02:24.473973", "params": {"makerelabund": "\"false\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.22\", \"0.26\"]", "groups": "[\"forest\", \"pasture\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"zscore\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28697", "id": "3511dc9f211ca562", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_normalize_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "87078348debd31f2"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "87078348debd31f2", "uuid": "9ff0bf1b-34a4-4486-a449-18e55d1e5577"}}, "update_time": "2018-02-08T18:02:47.222922", "tool_id": "mothur_otu_association", "outputs": {"__new_primary_file_unique.pearson|0.21.pearson__": {"src": "hda", "id": "c1f9b7f85ff447a6", "uuid": "a1aac0c9-3045-45c0-836d-1493ca8e591e"}, "__new_primary_file_unique.pearson|0.09.pearson__": {"src": "hda", "id": "7d1fdfaaecdf4192", "uuid": "190d3ceb-dbac-42b7-86f2-431ef542ade1"}, "__new_primary_file_unique.pearson|0.14.pearson__": {"src": "hda", "id": "15af681009ecbcd4", "uuid": "829a2d25-1d1f-4bd1-a94f-728b71ed4a8b"}, "__new_primary_file_unique.pearson|0.17.pearson__": {"src": "hda", "id": "114f907721fad498", "uuid": "b8e86fe8-b44b-43dd-832c-ccf1c29b1b49"}, "__new_primary_file_unique.pearson|0.32.pearson__": {"src": "hda", "id": "5c5398d0729f4c9a", "uuid": "f52b9ec3-a517-4374-8f13-d04f44eb252d"}, "__new_primary_file_unique.pearson|0.02.pearson__": {"src": "hda", "id": "c236b8a59d75a9c2", "uuid": "27ad07c8-efeb-4c4b-9c95-a68738ffb41e"}, "__new_primary_file_unique.pearson|0.12.pearson__": {"src": "hda", 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"7fcc2597b7ad9954", "uuid": "c6309615-8880-49ce-b9f5-a386be8bc8b7"}, "__new_primary_file_unique.pearson|0.36.pearson__": {"src": "hda", "id": "b60f79d04dee2eec", "uuid": "9ca41100-7ad9-45e8-a03a-64df3b213dbf"}, "__new_primary_file_unique.pearson|0.24.pearson__": {"src": "hda", "id": "94b253c013da9d07", "uuid": "03736b3b-ccba-4d40-a0de-b6d3d1709a5d"}, "__new_primary_file_unique.pearson|0.05.pearson__": {"src": "hda", "id": "cfcb788085ab492e", "uuid": "18fc98fb-2238-46e4-91cf-9a318eb3207a"}, "__new_primary_file_unique.pearson|0.33.pearson__": {"src": "hda", "id": "6e262c2ae2545ffb", "uuid": "06429343-666a-449b-bc23-94c807213edf"}, "logfile": {"src": "hda", "id": "73ed1fba7da78f4b", "uuid": "b005fd48-2d12-4e18-8471-b6a413a03e5e"}, "__new_primary_file_unique.pearson|0.19.pearson__": {"src": "hda", "id": "bc441ceb5a3223e1", "uuid": "7d6a6527-1daa-4624-b0fb-de3377b58c4c"}, "__new_primary_file_unique.pearson|0.16.pearson__": {"src": "hda", "id": "aa452a61ad24963a", "uuid": "1393e52e-a590-4174-9947-e9794deb3a10"}, "__new_primary_file_unique.pearson|0.55.pearson__": {"src": "hda", "id": "872f8bbac826a355", "uuid": "62d76d7a-216e-471b-9bc0-7db49cc077a4"}, "__new_primary_file_unique.pearson|0.13.pearson__": {"src": "hda", "id": "9c4915c8de2f90d1", "uuid": "4509cd1a-0c95-422e-84f4-e9c9a57fb559"}, "__new_primary_file_unique.pearson|0.27.pearson__": {"src": "hda", "id": "632437ce271bb8aa", "uuid": "8aa8d928-c084-41ec-83e4-c597839d9da7"}, "__new_primary_file_unique.pearson|0.26.pearson__": {"src": "hda", "id": "a842af6d14177fe6", "uuid": "1fa98059-5386-4b6f-9794-9cff5e7c3e67"}, "__new_primary_file_unique.pearson|0.22.pearson__": {"src": "hda", "id": "01ae29ee518639b6", "uuid": "5a789cc3-468b-4649-a3f5-7428b8f80c58"}, "__new_primary_file_unique.pearson|0.07.pearson__": {"src": "hda", "id": "3ac2939147b22342", "uuid": "0676e856-b147-48a4-9137-565323c071b6"}, "__new_primary_file_unique.pearson|0.29.pearson__": {"src": "hda", "id": "56dae71a8dfd28e4", "uuid": "4972bf5f-dc51-4616-8368-13e49a8b2efe"}, "__new_primary_file_unique.pearson|0.06.pearson__": {"src": "hda", "id": "13d8dea9ad27b203", "uuid": "0bb6d052-9c47-4c2d-9ff6-253d68a9705a"}, "__new_primary_file_unique.pearson|0.23.pearson__": {"src": "hda", "id": "652cc733e38b3fd8", "uuid": "a9988dbd-1aa0-400a-b0e7-cdd1473ae7b7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > otu.association(shared=otu.dat,method=pearson)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.unique.pearson.otu.corr\notu.0.01.pearson.otu.corr\notu.0.02.pearson.otu.corr\notu.0.03.pearson.otu.corr\notu.0.04.pearson.otu.corr\notu.0.05.pearson.otu.corr\notu.0.06.pearson.otu.corr\notu.0.07.pearson.otu.corr\notu.0.08.pearson.otu.corr\notu.0.09.pearson.otu.corr\notu.0.10.pearson.otu.corr\notu.0.11.pearson.otu.corr\notu.0.12.pearson.otu.corr\notu.0.13.pearson.otu.corr\notu.0.14.pearson.otu.corr\notu.0.15.pearson.otu.corr\notu.0.16.pearson.otu.corr\notu.0.17.pearson.otu.corr\notu.0.18.pearson.otu.corr\notu.0.19.pearson.otu.corr\notu.0.20.pearson.otu.corr\notu.0.21.pearson.otu.corr\notu.0.22.pearson.otu.corr\notu.0.23.pearson.otu.corr\notu.0.24.pearson.otu.corr\notu.0.25.pearson.otu.corr\notu.0.26.pearson.otu.corr\notu.0.27.pearson.otu.corr\notu.0.29.pearson.otu.corr\notu.0.32.pearson.otu.corr\notu.0.33.pearson.otu.corr\notu.0.36.pearson.otu.corr\notu.0.38.pearson.otu.corr\notu.0.41.pearson.otu.corr\notu.0.45.pearson.otu.corr\notu.0.55.pearson.otu.corr\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2039.dat' otu.dat && ln -s 'None' metadata.dat &&  echo 'otu.association( shared=otu.dat ,method=pearson )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:02:41.990561", "params": {"cutoff": "\"\"", "dbkey": "\"hg17\"", "label": "null", "groups": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"pearson\"", "metadata": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28785", "id": "c068ba61abe27ec2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_otu_association.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "a97c4449eeee3c89"}, "method": "kendall", "groups": ["forest", "pasture"], "label": ["0.03", "0.05", "0.36", "0.41", "0.55"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "a97c4449eeee3c89", "uuid": "2cc5e442-b3e7-4d4d-a33e-e8686510537f"}}, "update_time": "2018-02-08T18:03:05.842709", "tool_id": "mothur_otu_association", "outputs": {"__new_primary_file_0.55.kendall|0.05.kendall__": {"src": "hda", "id": "4f7f3fb5673240e3", "uuid": "75bfd5a1-ecd4-40d3-86d3-f46714fb2c06"}, "__new_primary_file_0.55.kendall|0.36.kendall__": {"src": "hda", "id": "b3f5ff2369d9d249", "uuid": "9750ce01-eeb2-49e6-bc87-8c742b5f7aca"}, "__new_primary_file_0.55.kendall|0.55.kendall__": {"src": "hda", "id": "9a70aaebc3d20bdd", "uuid": "96a76da6-1781-4a91-a55d-932954e630a4"}, "__new_primary_file_0.55.kendall|0.41.kendall__": {"src": "hda", "id": "d821d43764c03acb", "uuid": "5afaa011-1328-4ec7-9993-beebf0e70c38"}, "logfile": {"src": "hda", "id": "f7caa003b2842495", "uuid": "1d334062-244f-40a8-9707-99ea5d501792"}, "__new_primary_file_0.55.kendall|0.03.kendall__": {"src": "hda", "id": "664177380bb275d4", "uuid": "d146fe80-0495-49b1-8eb0-74d10be9c287"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > otu.association(relabund=otu.dat,label=0.03-0.05-0.36-0.41-0.55,groups= \rforest-pasture,method=kendall)\n0.03\n0.05\n0.36\n0.41\n0.55\n\nOutput File Names: \notu.0.03.kendall.otu.corr\notu.0.05.kendall.otu.corr\notu.0.36.kendall.otu.corr\notu.0.41.kendall.otu.corr\notu.0.55.kendall.otu.corr\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2077.dat' otu.dat && ln -s 'None' metadata.dat &&  echo 'otu.association( relabund=otu.dat ,label=0.03-0.05-0.36-0.41-0.55 ,groups=forest-pasture ,method=kendall )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:03:02.491040", "params": {"cutoff": "\"\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.36\", \"0.41\", \"0.55\"]", "groups": "[\"forest\", \"pasture\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "method": "\"kendall\"", "metadata": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28873", "id": "aa43a28a12fcf867", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_otu_association.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"label1": "0.05", "label2": "0.03", "otu": {"src": "hda", "id": "8b1e72fab2ca9b47"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "8b1e72fab2ca9b47", "uuid": "ae2d5b50-ae44-4ed1-b9bf-1406cf8f52a4"}}, "update_time": "2018-02-08T18:03:26.014987", "tool_id": "mothur_otu_hierarchy", "outputs": {"hierarchy": {"src": "hda", "id": "143cb76ef3d4aedc", "uuid": "c008d314-8736-4660-bacf-06cd5e994100"}, "logfile": {"src": "hda", "id": "e4517ef02489f4b1", "uuid": "e4848545-6f0c-4a9f-b6b9-540bfef39a71"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > otu.hierarchy(list=otu.dat,label=0.05-0.03,output=name)\n\nOutput File Names: \notu.0.03._.0.05.otu.hierarchy\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2084.dat' otu.dat &&  echo 'otu.hierarchy( list=otu.dat, label=0.05-0.03, output=name )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:03:22.868182", "params": {"label1": "\"0.05\"", "label2": "\"0.03\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "output": "\"name\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "28961", "id": "bb9931d062678360", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_otu_hierarchy.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"cutoff": "0.0", "countends": true, "align": "needleman", "scoring|setby": "default", "output": "", "fasta": {"src": "hda", "id": "68cdc65b079e45ae"}, "calc": ""}, "job": {"inputs": {"fasta": {"src": "hda", "id": "68cdc65b079e45ae", "uuid": "a7869ff0-be51-454d-b445-4196d2c581e8"}}, "update_time": "2018-02-08T18:03:58.606414", "tool_id": "mothur_pairwise_seqs", "outputs": {"logfile": {"src": "hda", "id": "af3d6ad9d44f4b02", "uuid": "c4bc8b57-1e3c-4ef7-8950-19ac34479089"}, "out_dist": {"src": "hda", "id": "ff2fd427cb51c4ed", "uuid": "06c4d160-9614-45c9-a917-495ada390c3d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pairwise.seqs(fasta=fasta.dat,align=needleman,processors=1)\n\nUsing 1 processors.\nProcessing sequences from fasta.dat ...\n0\t0\n95\t15\nIt took 15 to calculate the distances for 96 sequences.\n\nOutput File Names: \nfasta.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2087.dat' fasta.dat &&  echo 'pairwise.seqs( fasta=fasta.dat, align=needleman,  processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:03:40.313049", "params": {"scoring": "{\"setby\": \"default\", \"__current_case__\": 0}", "cutoff": "\"0.0\"", "countends": "\"true\"", "align": "\"needleman\"", "dbkey": "\"hg17\"", "output": "\"\"", "calc": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29057", "id": "76880adb125efe03", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pairwise_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"cutoff": "0.01", "countends": false, "align": "gotoh", "scoring|gapopen": "-2", "scoring|mismatch": "-1", "scoring|match": "2", "output": "lt", "fasta": {"src": "hda", "id": "5b02825370c62dc1"}, "calc": "onegap", "scoring|gapextend": "-1", "scoring|setby": "user"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "5b02825370c62dc1", "uuid": "88a82267-fcb7-4a89-99f7-e5a2f4d6d863"}}, "update_time": "2018-02-08T18:04:36.354756", "tool_id": "mothur_pairwise_seqs", "outputs": {"logfile": {"src": "hda", "id": "fccad1b547140dd3", "uuid": "9d3772a7-d94e-4aa0-9c2c-ce4092e51ef0"}, "out_dist": {"src": "hda", "id": "41944e51b7eea955", "uuid": "1cdb9228-8450-4900-a3e2-f1f9e88e38a9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pairwise.seqs(fasta=fasta.dat,align=gotoh,calc=onegap,countends=false,c \rutoff=0.01,match=2,mismatch=-1,gapopen=-2,gapextend=-1,output=lt,processors=1)\n\nUsing 1 processors.\nProcessing sequences from fasta.dat ...\n0\t0\n95\t18\nIt took 18 to calculate the distances for 96 sequences.\n\nOutput File Names: \nfasta.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2090.dat' fasta.dat &&  echo 'pairwise.seqs( fasta=fasta.dat, align=gotoh, calc=onegap, countends=false, cutoff=0.01, match=2, mismatch=-1, gapopen=-2, gapextend=-1, output=lt, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:04:14.828791", "params": {"scoring": "{\"gapopen\": \"-2\", \"mismatch\": \"-1\", \"__current_case__\": 1, \"setby\": \"user\", \"gapextend\": \"-1\", \"match\": \"2\"}", "cutoff": "\"0.01\"", "countends": "\"false\"", "align": "\"gotoh\"", "dbkey": "\"hg17\"", "output": "\"lt\"", "calc": "\"onegap\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29149", "id": "d36e0ad5b4ecc523", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pairwise_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "8afc4a870dadbd7d"}, "otu": {"src": "hda", "id": "31dbd8c6e9452ac3"}}, "job": {"inputs": {"group": {"src": "hda", "id": "8afc4a870dadbd7d", "uuid": "25515fae-47a6-4415-b726-2fca639df012"}, "otu": {"src": "hda", "id": "31dbd8c6e9452ac3", "uuid": "8f530433-634c-450d-a355-5baccd582764"}}, "update_time": "2018-02-08T18:05:00.623647", "tool_id": "mothur_parse_list", "outputs": {"__new_primary_file_pasture.unique|forest.0.13__": {"src": "hda", "id": "a85c51ad73ace21c", "uuid": "6a23b166-7009-4719-b04c-ffa7759be524"}, "__new_primary_file_pasture.unique|pasture.0.12__": {"src": "hda", "id": "3c9aa8dc96dd4037", "uuid": "cf71aa9d-2a2b-4b2c-aec0-2db9f47dc1b5"}, "__new_primary_file_pasture.unique|forest.0.06__": {"src": "hda", "id": "7407f06b1e052c43", "uuid": "47a0ec11-c781-4b0c-bbf4-2bb9f195e479"}, "__new_primary_file_pasture.unique|pasture.0.03__": {"src": "hda", "id": "afb54b8f1c8a1903", "uuid": "56eb91fa-64a2-486b-b9e9-f5a08781d96f"}, "__new_primary_file_pasture.unique|pasture.0.15__": {"src": "hda", "id": "a8ff40a3a195a77b", "uuid": "2a43e9cb-4686-4340-bce7-fecf5fc11fcc"}, "__new_primary_file_pasture.unique|forest.0.12__": {"src": "hda", "id": "57e39bb156480887", "uuid": "118bfa82-db72-4d78-98db-3b4ab0317f5f"}, "__new_primary_file_pasture.unique|forest.0.19__": {"src": "hda", "id": "3a89aaf65b4da934", "uuid": "38235792-7034-4faf-95a0-d62535622980"}, "__new_primary_file_pasture.unique|pasture.0.41__": {"src": "hda", "id": "686eaf07510a6daf", "uuid": "cc0ac23e-6c7a-4939-950f-8b014748f64c"}, "__new_primary_file_pasture.unique|forest.0.15__": {"src": "hda", "id": "03658f5433e82a2e", "uuid": "550438fa-1846-4449-9298-e05def3a211d"}, "__new_primary_file_pasture.unique|pasture.0.08__": {"src": "hda", "id": "bf4177214178aaac", "uuid": "6530c0a2-e3aa-4d5e-9e00-94a7eb76eebf"}, "__new_primary_file_pasture.unique|pasture.0.27__": {"src": "hda", "id": "ec73fd31f7fdd7ff", "uuid": "df4c822c-04d1-4daf-83d3-631aa695b6bf"}, "__new_primary_file_pasture.unique|forest.0.20__": {"src": "hda", "id": "947633482a2c76a9", "uuid": "645bfcc6-1f94-4944-a8e5-348033e8c9a5"}, "__new_primary_file_pasture.unique|forest.0.14__": {"src": "hda", "id": "387443286670d506", "uuid": "cc1c344e-c0e2-4b5d-8e9c-499b01b40486"}, "__new_primary_file_pasture.unique|forest.0.32__": {"src": "hda", "id": "ac851b4ae8518708", "uuid": "166ce5e6-b08d-40cb-88bf-038d4f768d59"}, "__new_primary_file_pasture.unique|pasture.0.13__": {"src": "hda", "id": "ca88bfbe9bd4fae9", "uuid": "6550f023-a974-4444-814c-5c14fbfd6dc3"}, "__new_primary_file_pasture.unique|pasture.0.09__": {"src": "hda", "id": "201c302e615535c1", "uuid": "0d637c85-d3ac-4c65-92fb-19b9d456ec3d"}, "__new_primary_file_pasture.unique|pasture.0.26__": {"src": "hda", "id": "7cec0fee27e98af5", "uuid": "7814f8bd-1d47-4b38-9e7d-4fb2433a3ad2"}, 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"\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > parse.list(list=otu.dat,group=group.dat)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.forest.unique.list\notu.pasture.unique.list\notu.forest.0.01.list\notu.pasture.0.01.list\notu.forest.0.02.list\notu.pasture.0.02.list\notu.forest.0.03.list\notu.pasture.0.03.list\notu.forest.0.04.list\notu.pasture.0.04.list\notu.forest.0.05.list\notu.pasture.0.05.list\notu.forest.0.06.list\notu.pasture.0.06.list\notu.forest.0.07.list\notu.pasture.0.07.list\notu.forest.0.08.list\notu.pasture.0.08.list\notu.forest.0.09.list\notu.pasture.0.09.list\notu.forest.0.10.list\notu.pasture.0.10.list\notu.forest.0.11.list\notu.pasture.0.11.list\notu.forest.0.12.list\notu.pasture.0.12.list\notu.forest.0.13.list\notu.pasture.0.13.list\notu.forest.0.14.list\notu.pasture.0.14.list\notu.forest.0.15.list\notu.pasture.0.15.list\notu.forest.0.16.list\notu.pasture.0.16.list\notu.forest.0.17.list\notu.pasture.0.17.list\notu.forest.0.18.list\notu.pasture.0.18.list\notu.forest.0.19.list\notu.pasture.0.19.list\notu.forest.0.20.list\notu.pasture.0.20.list\notu.forest.0.21.list\notu.pasture.0.21.list\notu.forest.0.22.list\notu.pasture.0.22.list\notu.forest.0.23.list\notu.pasture.0.23.list\notu.forest.0.24.list\notu.pasture.0.24.list\notu.forest.0.25.list\notu.pasture.0.25.list\notu.forest.0.26.list\notu.pasture.0.26.list\notu.forest.0.27.list\notu.pasture.0.27.list\notu.forest.0.29.list\notu.pasture.0.29.list\notu.forest.0.32.list\notu.pasture.0.32.list\notu.forest.0.33.list\notu.pasture.0.33.list\notu.forest.0.36.list\notu.pasture.0.36.list\notu.forest.0.38.list\notu.pasture.0.38.list\notu.forest.0.41.list\notu.pasture.0.41.list\notu.forest.0.45.list\notu.pasture.0.45.list\notu.forest.0.55.list\notu.pasture.0.55.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2093.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2094.dat' group.dat && ln -s 'None' count.dat &&  echo 'parse.list( list=otu.dat, group=group.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:04:52.955670", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29272", "id": "d1010cb72bf991e5", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_parse_list.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "e26b78b0e6def9bf"}, "otu": {"src": "hda", "id": "c7007f9410f08c64"}, "label": ["0.03", "0.05"]}, "job": {"inputs": {"group": {"src": "hda", "id": "e26b78b0e6def9bf", "uuid": "353c7160-a417-41fe-9d37-24159b022544"}, "otu": {"src": "hda", "id": "c7007f9410f08c64", "uuid": "0232831f-981d-49df-a50a-dabcf1d42762"}}, "update_time": "2018-02-08T18:05:28.674033", "tool_id": "mothur_parse_list", "outputs": {"__new_primary_file_pasture.0.05|pasture.0.03__": {"src": "hda", "id": "a3a2a175eac37c19", "uuid": "8bf3d63a-41e5-4a62-94d6-9d03c0ce81da"}, "__new_primary_file_pasture.0.05|forest.0.05__": {"src": "hda", "id": "9d88bce42e8c40da", "uuid": "ac2a67fa-77a2-4541-b7f7-bcb08303b8db"}, "logfile": {"src": "hda", "id": "3253f225acee3abb", "uuid": "ab23c433-574e-4176-8076-26879bc1ec86"}, "__new_primary_file_pasture.0.05|forest.0.03__": {"src": "hda", "id": "41d22b61843cac3f", "uuid": "0ecb66d9-a4c4-49fd-aaaf-0acca12e6040"}, "__new_primary_file_pasture.0.05|pasture.0.05__": {"src": "hda", "id": "defef927024814c1", "uuid": "5264fd79-68a4-43fa-8ef4-a5b5173ca3ea"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > parse.list(list=otu.dat,label=0.03-0.05,group=group.dat)\n0.03\n0.05\n\nOutput File Names: \notu.forest.0.03.list\notu.pasture.0.03.list\notu.forest.0.05.list\notu.pasture.0.05.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2168.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2169.dat' group.dat && ln -s 'None' count.dat &&  echo 'parse.list( list=otu.dat, label=0.03-0.05, group=group.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:05:25.394023", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29383", "id": "731d7fc7f6176125", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_parse_list.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"iters": "1000", "group": {"src": "hda", "id": "8ad407aea9325e76"}, "tree": {"src": "hda", "id": "44f326e1f448e78e"}, "name": {"src": "hda", "id": "97c6d122e81a6846"}, "groups": ["green", "orange"]}, "job": {"inputs": {"group": {"src": "hda", "id": "8ad407aea9325e76", "uuid": "9afc0a9e-9933-453c-9ab5-2fe30abaa2a5"}, "tree": {"src": "hda", "id": "44f326e1f448e78e", "uuid": "cf76b161-6124-4cb0-9ca4-e8882434ae2f"}, "name": {"src": "hda", "id": "97c6d122e81a6846", "uuid": "fad7abb3-74cd-46a0-9322-375ac06a7c01"}}, "update_time": "2018-02-08T18:05:47.450319", "tool_id": "mothur_parsimony", "outputs": {"psummary": {"src": "hda", "id": "483b2e2bc94213c3", "uuid": "9d5ba257-ce53-4043-aa08-6f39cdf6e5c8"}, "logfile": {"src": "hda", "id": "9d39ac49f9104593", "uuid": "b181eea4-4af0-4ef3-a44d-4e7b460501ca"}, "parsimony": {"src": "hda", "id": "4af28ef0562c6c37", "uuid": "7812f1e8-93bf-4e9f-992b-ef1acae68b9d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > parsimony(tree=tree.dat,iters=1000,group=group.dat,name=name.dat,proces \rsors=1)\n\nUsing 1 processors.\n********************#****#****#****#****#****#****#****#****#****#****#\nComparing to random:||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\nTree#\tGroups\tParsScore\tParsSig\n1\tgreen-orange\t1\t1\n\n\nOutput File Names: \ntree.dat.parsimony\ntree.dat.psummary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2175.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2176.dat' group.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2177.dat' name.dat &&  echo 'parsimony( tree=tree.dat, iters=1000, group=group.dat, name=name.dat, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:05:44.236142", "params": {"count": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29525", "id": "2768baa09f52abc1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_parsimony.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "1dcb63b7594c0a53"}, "groups": ["forest", "pasture"], "label": ["0.22", "0.55"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "1dcb63b7594c0a53", "uuid": "a2a67477-8ad3-4223-ae96-7001aeb2c40c"}}, "update_time": "2018-02-08T18:06:09.968465", "tool_id": "mothur_pca", "outputs": {"logfile": {"src": "hda", "id": "56e06f89792449a5", "uuid": "5af0509a-8a5f-476a-813e-b59c99931dcc"}, "__new_primary_file_0.55|0.22__": {"src": "hda", "id": "29057053eabeecf0", "uuid": "a6491f79-3680-4a2d-b5d6-2f64c3ee6145"}, "__new_primary_file_0.55|0.55__": {"src": "hda", "id": "009d092a3f629c9d", "uuid": "6e201424-5c1f-460f-943f-1ae330180131"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pca(shared=otu.dat,label=0.22-0.55,groups=forest-pasture,metric=true)\n\nProcessing 0.22\nRsq 1 axis: 0\nRsq 2 axis: 0\nRsq 3 axis: 0\n\nProcessing 0.55\nRsq 1 axis: 0\nRsq 2 axis: 0\nRsq 3 axis: 0\n\nOutput File Names: \notu.0.22.pca.axes\notu.0.22.pca.loadings\notu.0.55.pca.axes\notu.0.55.pca.loadings\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2181.dat' otu.dat &&  echo 'pca( shared=otu.dat, label=0.22-0.55, groups=forest-pasture, metric=true )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:06:06.690813", "params": {"metric": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "[\"forest\", \"pasture\"]", "label": "[\"0.22\", \"0.55\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29614", "id": "f4b2790380ce04e0", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pca.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"phylip": {"src": "hda", "id": "3b036687d3b15bc3"}}, "job": {"inputs": {"phylip": {"src": "hda", "id": "3b036687d3b15bc3", "uuid": "66da62a2-02ab-4a91-be6c-7c70de565a19"}}, "update_time": "2018-02-08T18:06:32.566231", "tool_id": "mothur_pcoa", "outputs": {"loadings": {"src": "hda", "id": "98b8d8437f7c5552", "uuid": "d5956ef8-bd0d-4945-b284-133ec75977e2"}, "logfile": {"src": "hda", "id": "8648246ff30fc2ff", "uuid": "ed6046d3-743c-47a4-beaa-bf7e553cd006"}, "pcoa": {"src": "hda", "id": "07469086593c8cef", "uuid": "5b7c51a9-9f60-474b-9a97-ad62f9075f8b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pcoa(phylip=phylip.dat,metric=true)\n\nProcessing...\nRsq 1 axis: 0.200353\nRsq 2 axis: 0.413022\nRsq 3 axis: 0.430959\n\nOutput File Names: \nphylip.pcoa.axes\nphylip.pcoa.loadings\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2187.dat' phylip.dat &&  echo 'pcoa( phylip=phylip.dat, metric=true )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:06:29.476405", "params": {"metric": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29703", "id": "1e4cd37e942f1647", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pcoa.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"trim|method": "position", "keepdots": true, "trim|start": "0", "pdiffs": "0", "fasta": {"src": "hda", "id": "ff8a6faa7e9cbc52"}, "trim|end": "0"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "ff8a6faa7e9cbc52", "uuid": "a94786f1-845b-43c2-9fa4-8e6317262ac5"}}, "update_time": "2018-02-08T18:06:45.075942", "tool_id": "mothur_pcr_seqs", "outputs": {"pcr_fasta": {"src": "hda", "id": "1d3a87989430d70d", "uuid": "28ee543c-eda1-4753-ab66-6276df887cd4"}, "logfile": {"src": "hda", "id": "ca4fcaac5d3c0250", "uuid": "2f22eeaf-a736-430c-b68e-749a87271586"}, "scrap_fasta": {"src": "hda", "id": "69896066c3f7be04", "uuid": "c91b7e23-f408-4f74-962c-60bbc1f4759e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pcr.seqs(fasta=fasta.dat,start=0,pdiffs=0,rdiffs=0,processors=1)\n\nUsing 1 processors.\nProcessing sequence: 3\n\nOutput File Names: \nfasta.pcr.dat\n\n\nIt took 0 secs to screen 3 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2191.dat' fasta.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' taxonomy_in.dat &&  echo 'pcr.seqs( fasta=fasta.dat, start=0, pdiffs=0, rdiffs=0,  processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:06:41.597226", "params": {"trim": "{\"start\": \"0\", \"end\": \"0\", \"method\": \"position\", \"__current_case__\": 2}", "keepdots": "\"true\"", "pdiffs": "\"0\"", "dbkey": "\"hg17\"", "rdiffs": "\"0\"", "group_in": "null", "taxonomy_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29791", "id": "9a68e8442a2ae0ec", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pcr_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"trim|method": "reference", "keepdots": false, "pdiffs": "2", "trim|ecoli": {"src": "hda", "id": "296c8570502f7d16"}, "fasta": {"src": "hda", "id": "296c8570502f7d16"}, "name_in": {"src": "hda", "id": "540d8ccadbb41cf8"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "296c8570502f7d16", "uuid": "9362aefb-8832-4e03-acd5-680564bde786"}, "ecoli": {"src": "hda", "id": "296c8570502f7d16", "uuid": "9362aefb-8832-4e03-acd5-680564bde786"}, "name_in": {"src": "hda", "id": "540d8ccadbb41cf8", "uuid": "e965dcc8-4320-413e-a48d-622e06334dae"}}, "update_time": "2018-02-08T18:07:16.938130", "tool_id": "mothur_pcr_seqs", "outputs": {"name_out": {"src": "hda", "id": "4e45b45a46840de7", "uuid": "ae7a5725-f8c7-4614-b22a-9b40d80745fc"}, "pcr_fasta": {"src": "hda", "id": "9b9da51b3cf3788c", "uuid": "5051221e-11db-45e7-b92a-9fe5b093f5e9"}, "logfile": {"src": "hda", "id": "b595ca7d5e4a4806", "uuid": "92c2c87b-8df3-4ce4-a91e-1ee540f139ba"}, "scrap_fasta": {"src": "hda", "id": "6566db4438049123", "uuid": "59a0a26d-b5b0-4a68-986d-821d65b390af"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pcr.seqs(fasta=fasta.dat,name=name_in.dat,ecoli=trim.ecoli.dat,pdiffs=2 \r,rdiffs=0,keepdots=false,processors=1)\n\nUsing 1 processors.\nProcessing sequence: 3\nRemoved 0 sequences from your name file.\n\nOutput File Names: \nfasta.pcr.dat\nname_in.pcr.dat\n\n\nIt took 0 secs to screen 3 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2196.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2197.dat' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' taxonomy_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2196.dat' trim.ecoli.dat &&  echo 'pcr.seqs( fasta=fasta.dat, name=name_in.dat, ecoli=trim.ecoli.dat, pdiffs=2, rdiffs=0, keepdots=false, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:07:13.398222", "params": {"trim": "{\"ecoli\": {\"values\": [{\"src\": \"hda\", \"id\": 2196}]}, \"method\": \"reference\", \"__current_case__\": 1}", "keepdots": "\"false\"", "pdiffs": "\"2\"", "dbkey": "\"hg17\"", "rdiffs": "\"0\"", "group_in": "null", "taxonomy_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "29923", "id": "7e283a4b4d60f5b4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pcr_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"trim|method": "oligos", "trim|oligos": {"src": "hda", "id": "a5b878b864addf4f"}, "group_in": {"src": "hda", "id": "a8982932cfaa9c91"}, "taxonomy_in": {"src": "hda", "id": "9c06f06735014421"}, "fasta": {"src": "hda", "id": "82820d47475784db"}, "name_in": {"src": "hda", "id": "9d35880b3bb3f3cb"}}, "job": {"inputs": {"group_in": {"src": "hda", "id": "a8982932cfaa9c91", "uuid": "66e3ae35-39b3-423e-b941-33461b54a7ad"}, "fasta": {"src": "hda", "id": "82820d47475784db", "uuid": "ceb90772-927b-440c-8052-73805f4ccb50"}, "taxonomy_in": {"src": "hda", "id": "9c06f06735014421", "uuid": "f15d0b71-c377-4c34-8371-bc21d18145a8"}, "name_in": {"src": "hda", "id": "9d35880b3bb3f3cb", "uuid": "564d66d5-2513-4e32-a3ba-dd22ef1f8415"}, "oligos": {"src": "hda", "id": "a5b878b864addf4f", "uuid": "0f5c7aab-d848-4e2a-992d-8983af54dd90"}}, "update_time": "2018-02-08T18:08:02.125280", "tool_id": "mothur_pcr_seqs", "outputs": {"accnos_out": {"src": "hda", "id": "c125545fbb84cf3f", "uuid": "afc10ef8-549d-46d6-9d0c-c126de31a2c5"}, "name_out": {"src": "hda", "id": "464ab120d73bbfdd", "uuid": "698fcaa6-b392-42c7-8fdf-381e07307454"}, "group_out": {"src": "hda", "id": "f8ee9f073d3c51fa", "uuid": "09c46081-7102-442e-8599-95f7369596f4"}, "taxonomy_out": {"src": "hda", "id": "d4da91f5a7beed4d", "uuid": "83fa36a7-fcb7-446d-8775-7224901b3c40"}, "scrap_fasta": {"src": "hda", "id": "daf83ea457bd17e1", "uuid": "209a1adf-26ab-4ca2-be19-af5749eb1cb9"}, "pcr_fasta": {"src": "hda", "id": "a103d4e65eccf231", "uuid": "75fffd97-8e82-4d4a-ae7f-f6e8e184586c"}, "logfile": {"src": "hda", "id": "5480ea63371d722e", "uuid": "62241193-8520-4216-9a1e-8f9969fa2327"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pcr.seqs(fasta=fasta.dat,name=name_in.dat,group=group_in.dat,taxonomy=t \raxonomy_in.dat,oligos=trim.oligos.dat,nomatch=reject,pdiffs=0,rdiffs=0,processor \rs=1)\n\nUsing 1 processors.\nProcessing sequence: 3\nRemoved 3 sequences from your name file.\nRemoved 3 sequences from your group file.\nRemoved 3 sequences from your taxonomy file.\n\nOutput File Names: \nfasta.pcr.dat\nfasta.bad.accnos\nfasta.scrap.pcr.dat\nname_in.pcr.dat\ngroup_in.pcr.dat\ntaxonomy_in.pcr.dat\n\n\nIt took 0 secs to screen 3 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2202.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2205.dat' name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2206.dat' group_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2204.dat' taxonomy_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2203.dat' trim.oligos.dat &&  echo 'pcr.seqs( fasta=fasta.dat, name=name_in.dat, group=group_in.dat, taxonomy=taxonomy_in.dat, oligos=trim.oligos.dat, nomatch=reject,  pdiffs=0, rdiffs=0,  processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:07:57.811767", "params": {"trim": "{\"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 2203}]}, \"keepprimer\": \"false\", \"method\": \"oligos\", \"__current_case__\": 0, \"nomatch\": \"reject\"}", "keepdots": "\"true\"", "dbkey": "\"hg17\"", "rdiffs": "\"0\"", "pdiffs": "\"0\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30108", "id": "b82be0a67dfc3ead", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pcr_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"grouping|use": "no", "tree": {"src": "hda", "id": "7b73c9ba1609e7c1"}}, "job": {"inputs": {"tree": {"src": "hda", "id": "7b73c9ba1609e7c1", "uuid": "6d09350d-19d7-4732-add6-9545698ec688"}}, "update_time": "2018-02-08T18:08:47.617108", "tool_id": "mothur_phylo_diversity", "outputs": {"logfile": {"src": "hda", "id": "a957edb6cc1a8c18", "uuid": "de495382-5ca6-4e53-836d-f49489766a65"}, "summary_out": {"src": "hda", "id": "19b2c8d8c6d10b1a", "uuid": "55aaf68f-798e-4b74-9e5b-1bc9f46456b4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > phylo.diversity(tree=tree.dat,iters=1000,freq=100.0,scale=false,collect \r=false,rarefy=false,summary=true,processors=1)\n\nUsing 1 processors.\nIt took 0 secs to run phylo.diversity.\n\nOutput File Names: \ntree.1.phylodiv.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2214.dat' tree.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'phylo.diversity( tree=tree.dat, iters=1000, freq=100.0, scale=false, collect=false, rarefy=false, summary=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:08:44.453569", "params": {"count": "null", "scale": "\"false\"", "name": "null", "iters": "\"1000\"", "rarefy": "\"false\"", "dbkey": "\"hg17\"", "summary": "\"true\"", "collect": "\"false\"", "freq": "\"100.0\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "grouping": "{\"use\": \"no\", \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30220", "id": "c097cce02f6efe06", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_phylo_diversity.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"grouping|group": {"src": "hda", "id": "a37203f14505a5c8"}, "tree": {"src": "hda", "id": "687d98d0d3ddbb66"}, "rarefy": true, "grouping|groups": ["orange", "green"], "collect": true, "grouping|use": "yes"}, "job": {"inputs": {"group": {"src": "hda", "id": "a37203f14505a5c8", "uuid": "2870715f-70ac-4788-a64c-0dfba78c0ed2"}, "tree": {"src": "hda", "id": "687d98d0d3ddbb66", "uuid": "13a48277-9c45-4c94-a7be-9689972e7ada"}}, "update_time": "2018-02-08T18:09:08.852562", "tool_id": "mothur_phylo_diversity", "outputs": {"rarefaction_out": {"src": "hda", "id": "d57c2a3df64722d8", "uuid": "b82bc970-f0bd-4e15-9227-204614fbc92f"}, "logfile": {"src": "hda", "id": "010d9b650278df16", "uuid": "dc09882d-c97c-4773-9ff0-78bd2e02bcde"}, "summary_out": {"src": "hda", "id": "7c14b8cbe6ecfd6a", "uuid": "0a80c49c-3f99-4742-addd-efafe3433cc5"}, "collectors_out": {"src": "hda", "id": "8609b632c86cf056", "uuid": "8019ed27-81e8-4730-bdf3-ef44cc51c37f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > phylo.diversity(tree=tree.dat,group=grouping.group.dat,iters=1000,freq= \r100.0,scale=false,collect=true,rarefy=true,summary=true,processors=1)\n\nUsing 1 processors.\nIt took 0 secs to run phylo.diversity.\n\nOutput File Names: \ntree.1.phylodiv.summary\ntree.1.phylodiv.rarefaction\ntree.1.phylodiv\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2217.dat' tree.dat && ln -s 'None' name.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2218.dat' grouping.group.dat &&  echo 'phylo.diversity( tree=tree.dat, group=grouping.group.dat, iters=1000, freq=100.0, scale=false, collect=true, rarefy=true, summary=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:09:05.222478", "params": {"count": "null", "scale": "\"false\"", "name": "null", "iters": "\"1000\"", "rarefy": "\"true\"", "dbkey": "\"hg17\"", "summary": "\"true\"", "collect": "\"true\"", "freq": "\"100.0\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "grouping": "{\"use\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 2218}]}, \"groups\": null, \"__current_case__\": 0}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30335", "id": "dad37bad3e582a03", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_phylo_diversity.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"taxonomy": {"src": "hda", "id": "d277a827d7315f6a"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "d277a827d7315f6a", "uuid": "64965276-ce26-4135-afc9-702956d01e25"}}, "update_time": "2018-02-08T18:09:39.122665", "tool_id": "mothur_phylotype", "outputs": {"rabund": {"src": "hda", "id": "ae543f1a0583f8de", "uuid": "80a208ce-97f3-4e0f-8213-f2234b6e2b58"}, "logfile": {"src": "hda", "id": "982a3dd88517c4ae", "uuid": "0f6b7512-e7e5-4631-af21-5ca5ab0fa359"}, "otulist": {"src": "hda", "id": "905d0f9f657a61a3", "uuid": "b6e5a5dd-bd2e-4caf-a2e9-58dad1375c99"}, "sabund": {"src": "hda", "id": "a05060b14eba45e1", "uuid": "1ab81d82-d202-475e-bee9-ba9efb8b4683"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > phylotype(taxonomy=taxonomy.dat)\n1\n2\n3\n4\n5\n6\n\nOutput File Names: \ntaxonomy.tx.sabund\ntaxonomy.tx.rabund\ntaxonomy.tx.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2223.dat' taxonomy.dat && ln -s 'None' name.dat &&  echo 'phylotype( taxonomy=taxonomy.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:09:35.816289", "params": {"cutoff": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\"", "label": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30429", "id": "66041b9fc316678f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_phylotype.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"taxonomy": {"src": "hda", "id": "9b8e3eac2c41c663"}, "cutoff": "5", "label": ["1", "4", "5"]}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "9b8e3eac2c41c663", "uuid": "e85d537c-b3b3-41ee-892f-a5c4380c1157"}}, "update_time": "2018-02-08T18:10:06.761247", "tool_id": "mothur_phylotype", "outputs": {"rabund": {"src": "hda", "id": "9633d2046ccd09af", "uuid": "87a5b313-4033-449a-823e-760b4c678d47"}, "logfile": {"src": "hda", "id": "eea2aea36ad87984", "uuid": "b1729cf2-133b-4726-9a90-dec25423d7af"}, "otulist": {"src": "hda", "id": "d32d60f54a1f25d7", "uuid": "0ad1d6ff-cbf5-4aa5-bb8f-0ef07d6f4155"}, "sabund": {"src": "hda", "id": "da701c510c7a233c", "uuid": "5b1e28a8-09d8-4043-80cc-d7188e013864"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > phylotype(taxonomy=taxonomy.dat,cutoff=5,label=1-4-5)\n1\n4\n5\n\nOutput File Names: \ntaxonomy.tx.sabund\ntaxonomy.tx.rabund\ntaxonomy.tx.list\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2228.dat' taxonomy.dat && ln -s 'None' name.dat &&  echo 'phylotype( taxonomy=taxonomy.dat ,cutoff=5 ,label=1-4-5 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:10:03.466586", "params": {"cutoff": "\"5\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\"", "label": "[\"1\", \"4\", \"5\"]"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30522", "id": "f39983d675d72056", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_phylotype.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "12970ab350c1c4c1"}, "name": {"src": "hda", "id": "9954064f1597ebe8"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "12970ab350c1c4c1", "uuid": "eeea6a4b-d253-4b79-b884-25c80efe11d2"}, "name": {"src": "hda", "id": "9954064f1597ebe8", "uuid": "aa55e0a2-e8ce-422e-91ea-9bef6ab0bff7"}}, "update_time": "2018-02-08T18:10:38.444598", "tool_id": "mothur_pre_cluster", "outputs": {"__new_primary_file_fasta|fasta__": {"src": "hda", "id": "64228473c8483b3a", "uuid": "9e959b52-5138-4af8-aa5f-ce6b5c6fe494"}, "logfile": {"src": "hda", "id": "3eccd2a5f82af3af", "uuid": "820915eb-6709-42dc-a244-e086ff84c973"}, "names_out": {"src": "hda", "id": "dd319f1126fd20f4", "uuid": "336785bd-3ca5-4a7e-9f23-35ac0956eab3"}, "fasta_out": {"src": "hda", "id": "9d62bd31039db014", "uuid": "82dd042c-1999-40cf-86e6-d0e0e1d319a6"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pre.cluster(fasta=fasta.dat,name=name.dat,diffs=1,match=1,mismatch=-1,g \rapopen=-2,gapextend=-1,topdown=true,processors=1)\n\nUsing 1 processors.\n0\t5\t0\n5\t5\t0\nTotal number of sequences before precluster was 5.\npre.cluster removed 0 sequences.\n\nIt took 0 secs to cluster 5 sequences.\n\nOutput File Names: \nfasta.precluster.dat\nfasta.precluster.names\nfasta.precluster.map\n\n\nmothur > quit\n>U68589\nTAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n>U68590\nTAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n>U68591\nCGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n>U68592\nTAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n>U68593\nTAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\n>U68589\nTAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n>U68590\nTAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n>U68591\nCGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n>U68592\nTAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n>U68593\nTAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\nideal_seq_1\t1\nU68589\t1\t0\tTAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n\nideal_seq_2\t1\nU68590\t1\t0\tTAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n\nideal_seq_3\t1\nU68591\t1\t0\tCGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n\nideal_seq_4\t1\nU68592\t1\t0\tTAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n\nideal_seq_5\t1\nU68593\t1\t0\tTAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\n\nU68589\tU68589\nU68590\tU68590\nU68591\tU68591\nU68592\tU68592\nU68593\tU68593\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2233.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2234.dat' name.dat && ln -s 'None' group.dat &&  echo 'pre.cluster( fasta=fasta.dat, name=name.dat, diffs=1, match=1, mismatch=-1, gapopen=-2, gapextend=-1, topdown=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log &&  cat fasta* &&  if [ -f fasta.precluster.map ]; then mv fasta.precluster.map fasta.precluster.fasta.map; fi", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:10:34.343955", "params": {"diffs": "\"1\"", "group": "null", "topdown": "\"true\"", "gapopen": "\"-2\"", "mismatch": "\"-1\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "gapextend": "\"-1\"", "match": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30644", "id": "acb17c34a39829bc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pre_cluster.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "50a92933398c2e4e"}, "name": {"src": "hda", "id": "4e38a27672f3cb4b"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "50a92933398c2e4e", "uuid": "883de2f2-5301-413e-a278-8d845b20062d"}, "name": {"src": "hda", "id": "4e38a27672f3cb4b", "uuid": "e07df41b-7fa8-46f1-a60e-ce78d88c9225"}}, "update_time": "2018-02-08T18:11:11.834281", "tool_id": "mothur_pre_cluster", "outputs": {"__new_primary_file_fasta|fasta__": {"src": "hda", "id": "a0dcd297bbc9a51b", "uuid": "482c1fa4-2755-4dab-8e1c-af59d8ea02c1"}, "logfile": {"src": "hda", "id": "3fffea1ce04dc068", "uuid": "b41f03ac-b8c9-49a3-90fc-541837d2c668"}, "count_out": {"src": "hda", "id": "ef0fbc54739e8d83", "uuid": "736eccac-1a6d-4663-8f24-6ec335df2110"}, "fasta_out": {"src": "hda", "id": "99645864eaeb63bc", "uuid": "574e34be-d03e-4896-99a9-10bb098d47c8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > pre.cluster(fasta=fasta.dat,count=name.dat,diffs=1,match=1,mismatch=-1, \rgapopen=-2,gapextend=-1,topdown=true,processors=1)\n\nUsing 1 processors.\n0\t5\t0\n5\t5\t0\nTotal number of sequences before precluster was 5.\npre.cluster removed 0 sequences.\n\nIt took 0 secs to cluster 5 sequences.\n\nOutput File Names: \nfasta.precluster.dat\nfasta.precluster.count_table\nfasta.precluster.map\n\n\nmothur > quit\n>U68589\nTAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n>U68590\nTAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n>U68591\nCGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n>U68592\nTAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n>U68593\nTAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\nRepresentative_Sequence\ttotal\nU68589\t1\nU68590\t1\nU68591\t1\nU68592\t1\nU68593\t1\n>U68589\nTAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n>U68590\nTAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n>U68591\nCGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n>U68592\nTAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n>U68593\nTAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\nideal_seq_1\t1\nU68589\t1\t0\tTAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n\nideal_seq_2\t1\nU68590\t1\t0\tTAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n\nideal_seq_3\t1\nU68591\t1\t0\tCGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n\nideal_seq_4\t1\nU68592\t1\t0\tTAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n\nideal_seq_5\t1\nU68593\t1\t0\tTAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\n\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2239.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2240.dat' name.dat && ln -s 'None' group.dat &&  echo 'pre.cluster( fasta=fasta.dat, count=name.dat, diffs=1, match=1, mismatch=-1, gapopen=-2, gapextend=-1, topdown=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log &&  cat fasta* &&  if [ -f fasta.precluster.map ]; then mv fasta.precluster.map fasta.precluster.fasta.map; fi", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:11:08.174971", "params": {"diffs": "\"1\"", "group": "null", "topdown": "\"true\"", "gapopen": "\"-2\"", "mismatch": "\"-1\"", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "gapextend": "\"-1\"", "match": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30761", "id": "bd5643b7bad6c5ee", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_pre_cluster.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otulabel": "Otu1", "fasta": {"src": "hda", "id": "f5f5b5fcc20d3bfb"}, "otu": {"src": "hda", "id": "605677fb26a1d5d5"}, "label": "0.30"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "f5f5b5fcc20d3bfb", "uuid": "0249750c-f281-46b5-843e-160d09ed0d5a"}, "otu": {"src": "hda", "id": "605677fb26a1d5d5", "uuid": "be246a42-2fea-4653-b9cf-d3fb15ca4900"}}, "update_time": "2018-02-08T18:11:45.843827", "tool_id": "mothur_primer_design", "outputs": {"logfile": {"src": "hda", "id": "7e1d0ae02135b35e", "uuid": "838f32be-609c-44d2-afae-f925ffd59147"}, "list_out": {"src": "hda", "id": "01b4d9af49cf5af2", "uuid": "74f50cd4-de52-4c80-bbab-12493bb9139f"}, "summary_out": {"src": "hda", "id": "61fd885aefd5193f", "uuid": "55010ccf-de2c-407a-b483-f17be1f1b8ef"}, "fasta_out": {"src": "hda", "id": "6df628d23dd00405", "uuid": "89ece71b-206a-48ac-81aa-55dfbf5e2f31"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > primer.design(fasta=fasta.dat,list=otu.dat,label=0.30,otulabel=Otu1,pdi \rffs=0,length=18,processors=1)\n\nUsing 1 processors.\n\nFinding consensus sequences for each otu...Done.\n\nIt took 1 secs to process 2 OTUs.\n\nOutput File Names: \notu.0.30.otu.cons.fasta\notu.0.30.primer.summary\notu.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2245.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2246.dat' otu.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'primer.design( fasta=fasta.dat, list=otu.dat, label=0.30, otulabel=Otu1, pdiffs=0, length=18, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:11:42.160085", "params": {"count": "null", "cutoff": "\"\"", "name": "null", "otulabel": "\"Otu1\"", "mintm": "\"\"", "length": "\"18\"", "dbkey": "\"hg17\"", "label": "\"0.30\"", "pdiffs": "\"0\"", "maxtm": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "30895", "id": "2e05a675c8e4effa", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_primer_design.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "970eee70888a4aa6"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "970eee70888a4aa6", "uuid": "ae7991ee-0c1b-4f75-b3d9-b55a0be692f8"}}, "update_time": "2018-02-08T18:12:16.539106", "tool_id": "mothur_rarefaction_shared", "outputs": {"logfile": {"src": "hda", "id": "49a829891848cb74", "uuid": "9c41a416-c997-4435-806e-17a51309f45e"}, "rarefaction": {"src": "hda", "id": "b5c3e3c24268afba", "uuid": "8d1c764c-846a-4fab-90c5-2e031d0581f9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > rarefaction.shared(shared=otu.dat,calc=sharedobserved,iters=1000)\nunique\t\n0.01\t\n0.02\t\n0.03\t\n0.04\t\n0.05\t\n0.06\t\n0.07\t\n0.08\t\n0.09\t\n0.10\t\n0.11\t\n0.12\t\n0.13\t\n0.14\t\n0.15\t\n0.16\t\n0.17\t\n0.18\t\n0.19\t\n0.20\t\n0.21\t\n0.22\t\n0.23\t\n0.24\t\n0.25\t\n0.26\t\n0.27\t\n0.29\t\n0.32\t\n0.33\t\n0.36\t\n0.38\t\n0.41\t\n0.45\t\n0.55\t\n\nOutput File Names: \notu.shared.rarefaction\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2251.dat' otu.dat &&  echo 'rarefaction.shared( shared=otu.dat, calc=sharedobserved, iters=1000  )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:12:13.076005", "params": {"iters": "\"1000\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"__current_case__\": 1, \"usess\": \"no\"}", "designc": "{\"usedesign\": \"no\", \"__current_case__\": 1}", "groups": "null", "jumble": "\"false\"", "calc": "\"sharedobserved\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31000", "id": "89c39e6bc9d1ed43", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_rarefaction_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"calc": ["sharedobserved", "sharednseqs"], "otu": {"src": "hda", "id": "3895de01123aa786"}, "groups": ["forest", "pasture"], "label": ["0.22", "0.55"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "3895de01123aa786", "uuid": "88a38bca-3103-4bda-81ea-699d70bd90d0"}}, "update_time": "2018-02-08T18:12:32.107121", "tool_id": "mothur_rarefaction_shared", "outputs": {"logfile": {"src": "hda", "id": "8261f0fefe52b3d8", "uuid": "5354b0af-28d8-460c-9093-62d09996e000"}, "rarefaction": {"src": "hda", "id": "2778f88774dcfec9", "uuid": "410e0a28-c294-4bdd-b96c-b61a50529113"}, "rarefaction2": {"src": "hda", "id": "1eaf0a2d8c29e47a", "uuid": "de7d8886-eeff-4af4-a8ed-5b282a2a569e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > rarefaction.shared(shared=otu.dat,label=0.22-0.55,groups=forest-pasture \r,calc=sharedobserved-sharednseqs,iters=1000)\n0.22\t\n0.55\t\n\nOutput File Names: \notu.shared.rarefaction\notu.shared.r_nseqs\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2254.dat' otu.dat &&  echo 'rarefaction.shared( shared=otu.dat, label=0.22-0.55, groups=forest-pasture, calc=sharedobserved-sharednseqs, iters=1000  )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:12:28.634254", "params": {"iters": "\"1000\"", "dbkey": "\"hg17\"", "label": "[\"0.22\", \"0.55\"]", "subsample": "{\"__current_case__\": 1, \"usess\": \"no\"}", "designc": "{\"usedesign\": \"no\", \"__current_case__\": 1}", "groups": "[\"forest\", \"pasture\"]", "jumble": "\"false\"", "calc": "[\"sharedobserved\", \"sharednseqs\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31087", "id": "5f0fd33b40be7b90", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_rarefaction_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"designc|sets": ["tardis", "dalek"], "designc|usedesign": "yes", "otu": {"src": "hda", "id": "8d08869cf0678e94"}, "designc|design": {"src": "hda", "id": "8e702b0abbcab5be"}}, "job": {"inputs": {"design": {"src": "hda", "id": "8e702b0abbcab5be", "uuid": "9cc7a81b-4869-448e-9751-e599dff8e2ac"}, "otu": {"src": "hda", "id": "8d08869cf0678e94", "uuid": "4254f44a-9b85-4acd-9b43-834923a84ca8"}}, "update_time": "2018-02-08T18:12:48.699173", "tool_id": "mothur_rarefaction_shared", "outputs": {"logfile": {"src": "hda", "id": "c2f3aa02e3d98e9a", "uuid": "4484d484-ce5c-4a20-a616-fb7694fbf3ae"}, "group_rarefaction": {"src": "hda", "id": "3c471526d7d3b609", "uuid": "df5365f0-a83d-4c34-898c-86bd2237bfd7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > rarefaction.shared(shared=otu.dat,design=designc.design.dat,sets=tardis \r-dalek,calc=sharedobserved,iters=1000)\nunique\tdalek\n0.01\tdalek\n0.02\tdalek\n0.03\tdalek\n0.04\tdalek\n0.05\tdalek\n0.06\tdalek\n0.07\tdalek\n0.08\tdalek\n0.09\tdalek\n0.10\tdalek\n0.11\tdalek\n0.12\tdalek\n0.13\tdalek\n0.14\tdalek\n0.15\tdalek\n0.16\tdalek\n0.17\tdalek\n0.18\tdalek\n0.19\tdalek\n0.20\tdalek\n0.21\tdalek\n0.22\tdalek\n0.23\tdalek\n0.24\tdalek\n0.25\tdalek\n0.26\tdalek\n0.27\tdalek\n0.29\tdalek\n0.32\tdalek\n0.33\tdalek\n0.36\tdalek\n0.38\tdalek\n0.41\tdalek\n0.45\tdalek\n0.55\tdalek\nunique\ttardis\n0.01\ttardis\n0.02\ttardis\n0.03\ttardis\n0.04\ttardis\n0.05\ttardis\n0.06\ttardis\n0.07\ttardis\n0.08\ttardis\n0.09\ttardis\n0.10\ttardis\n0.11\ttardis\n0.12\ttardis\n0.13\ttardis\n0.14\ttardis\n0.15\ttardis\n0.16\ttardis\n0.17\ttardis\n0.18\ttardis\n0.19\ttardis\n0.20\ttardis\n0.21\ttardis\n0.22\ttardis\n0.23\ttardis\n0.24\ttardis\n0.25\ttardis\n0.26\ttardis\n0.27\ttardis\n0.29\ttardis\n0.32\ttardis\n0.33\ttardis\n0.36\ttardis\n0.38\ttardis\n0.41\ttardis\n0.45\ttardis\n0.55\ttardis\n\nOutput File Names: \notu.groups.rarefaction\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2258.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2259.dat' designc.design.dat &&  echo 'rarefaction.shared( shared=otu.dat, design=designc.design.dat, sets=tardis-dalek, calc=sharedobserved, iters=1000  )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:12:45.102451", "params": {"iters": "\"1000\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"__current_case__\": 1, \"usess\": \"no\"}", "designc": "{\"usedesign\": \"yes\", \"design\": {\"values\": [{\"src\": \"hda\", \"id\": 2259}]}, \"__current_case__\": 0, \"sets\": [\"tardis\", \"dalek\"]}", "groups": "null", "jumble": "\"false\"", "calc": "\"sharedobserved\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31201", "id": "8cf2c4d96fac8f30", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_rarefaction_shared.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "8a6106ba2478bdbd"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "8a6106ba2478bdbd", "uuid": "0f90ab92-22ce-4056-8a79-dcd71b3eeb92"}}, "update_time": "2018-02-08T18:13:04.886441", "tool_id": "mothur_rarefaction_single", "outputs": {"logfile": {"src": "hda", "id": "b15916a29e3c3d1e", "uuid": "52b8eb55-fb32-4e5d-8207-a3baa4c9d25e"}, "__new_primary_file_sobs|sobs__": {"src": "hda", "id": "5d9e2e480e0229ed", "uuid": "fd7ca367-f723-483b-a814-f0c35e2270b3"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > rarefaction.single(shared=otu.dat,calc=sobs,abund=10,iters=1000,freq=10 \r0.0,processors=1)\n\nUsing 1 processors.\n\nProcessing group forest\n\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nProcessing group pasture\n\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.groups.rarefaction\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2262.dat' otu.dat &&  echo 'rarefaction.single( shared=otu.dat, calc=sobs, abund=10, iters=1000, freq=100.0, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log  && mv otu\\.*rarefaction otu.r_sobs", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:13:00.863804", "params": {"abund": "\"10\"", "iters": "\"1000\"", "dbkey": "\"hg17\"", "label": "null", "freq": "\"100.0\"", "calc": "\"sobs\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31288", "id": "aaec100bcea4a774", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_rarefaction_single.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"calc": ["ace", "bootstrap", "chao", "jack", "sobs", "simpsoneven", "shannoneven", "heip", "smithwilson", "coverage", "simpson", "invsimpson", "shannon", "npshannon", "nseqs"], "otu": {"src": "hda", "id": "d8c76c99cfcf0ce5"}, "label": ["0.03", "0.05", "0.36", "0.55"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "d8c76c99cfcf0ce5", "uuid": "f8adb6cf-945c-4639-90f4-153241a99cb3"}}, "update_time": "2018-02-08T18:13:25.506137", "tool_id": "mothur_rarefaction_single", "outputs": {"__new_primary_file_sobs|coverage__": {"src": "hda", "id": "3b7ff9e5c7d690b4", "uuid": "8a034c17-5081-444f-9a9e-174ebd07999d"}, "__new_primary_file_sobs|shannon__": {"src": "hda", "id": "e3b08db904631c4c", "uuid": "6f3a3840-7c8b-49ae-a8dc-b24a34691cdb"}, "__new_primary_file_sobs|ace__": {"src": "hda", "id": "f45423591c0f7733", "uuid": "85350342-20d0-4e47-94ce-561b936f8e75"}, "__new_primary_file_sobs|nseqs__": {"src": "hda", "id": "bc738157a4fad361", "uuid": "2c68d624-9dba-4141-8051-641f9405fb5a"}, "__new_primary_file_sobs|invsimpson__": {"src": "hda", "id": "b0defc02722ab4d6", "uuid": "b39df22c-4d22-4ecc-a4d4-fea145725628"}, "__new_primary_file_sobs|bootstrap__": {"src": "hda", "id": "8b044c65de596171", "uuid": "f5a42c19-8c80-4ebf-8bc3-a5e7a778393d"}, "__new_primary_file_sobs|smithwilson__": {"src": "hda", "id": "cbfc85f745f39a3e", "uuid": "33ce0af3-307b-4fa7-8df6-75627e428aa1"}, "__new_primary_file_sobs|heip__": {"src": "hda", "id": "16ff13d461ecce2e", "uuid": "2732840c-8e2c-4b39-8acb-20145fb3a2a1"}, "__new_primary_file_sobs|sobs__": {"src": "hda", "id": "901603caef1d8ee8", "uuid": "28bfa969-271e-43ed-b4f9-ec078107ea7d"}, "__new_primary_file_sobs|shannoneven__": {"src": "hda", "id": "c556bb1d585cd085", "uuid": "bcdf20c5-5987-4889-b27c-d9edd5204e1a"}, "__new_primary_file_sobs|simpsoneven__": {"src": "hda", "id": "0de71dd17c089dd9", "uuid": "5d8b588c-00e4-4d82-a6fb-83eb5cd9d27b"}, "__new_primary_file_sobs|chao__": {"src": "hda", "id": "d4a5fd64bf471cbc", "uuid": "bfb3c23f-8324-40a5-8fcc-c6f06ca92700"}, "__new_primary_file_sobs|jack__": {"src": "hda", "id": "adb88159fa7b3775", "uuid": "cc7c2da1-c45e-4fc5-91ea-9c66cbe6b06e"}, "__new_primary_file_sobs|npshannon__": {"src": "hda", "id": "47f7483d27dc8522", "uuid": "101cf724-e313-4e6c-bd51-b830e86b8dde"}, "logfile": {"src": "hda", "id": "70d430aeade00c09", "uuid": "cae16ed2-c51a-4ba7-a8b7-822fd4f265c1"}, "__new_primary_file_sobs|simpson__": {"src": "hda", "id": "2091b9e5d015e899", "uuid": "ff84dee4-e777-4d24-a760-e151adf22e3d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > rarefaction.single(shared=otu.dat,label=0.03-0.05-0.36-0.55,calc=ace-bo \rotstrap-chao-jack-sobs-simpsoneven-shannoneven-heip-smithwilson-coverage-simpson \r-invsimpson-shannon-npshannon-nseqs,abund=10,iters=1000,freq=100.0,processors=1) \r\u001b[A\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[K)\n\nUsing 1 processors.\n\nProcessing group forest\n\n0.03\n0.05\n0.36\n0.55\n\nProcessing group pasture\n\n0.03\n0.05\n0.36\n0.55\n\nOutput File Names: \notu.groups.r_ace\notu.groups.r_bootstrap\notu.groups.r_chao\notu.groups.r_coverage\notu.groups.r_heip\notu.groups.r_invsimpson\notu.groups.r_jack\notu.groups.r_npshannon\notu.groups.r_nseqs\notu.groups.r_shannon\notu.groups.r_shannoneven\notu.groups.r_simpson\notu.groups.r_simpsoneven\notu.groups.r_smithwilson\notu.groups.rarefaction\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2265.dat' otu.dat &&  echo 'rarefaction.single( shared=otu.dat, label=0.03-0.05-0.36-0.55, calc=ace-bootstrap-chao-jack-sobs-simpsoneven-shannoneven-heip-smithwilson-coverage-simpson-invsimpson-shannon-npshannon-nseqs, abund=10, iters=1000, freq=100.0, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log  && mv otu\\.*rarefaction otu.r_sobs", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:13:21.254753", "params": {"abund": "\"10\"", "iters": "\"1000\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.36\", \"0.55\"]", "freq": "\"100.0\"", "calc": "[\"ace\", \"bootstrap\", \"chao\", \"jack\", \"sobs\", \"simpsoneven\", \"shannoneven\", \"heip\", \"smithwilson\", \"coverage\", \"simpson\", \"invsimpson\", \"shannon\", \"npshannon\", \"nseqs\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31377", "id": "ed97b3e2ab207f95", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_rarefaction_single.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input|dist": {"src": "hda", "id": "9377ba4c4b447a14"}, "input|source": "phylip", "accnos": {"src": "hda", "id": "9963fdf634013460"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "9963fdf634013460", "uuid": "b928989e-2b62-415c-bff5-74f13a5d7c34"}, "dist": {"src": "hda", "id": "9377ba4c4b447a14", "uuid": "6ecd1791-70d0-43da-8f83-310f7c259672"}}, "update_time": "2018-02-08T18:13:48.134708", "tool_id": "mothur_remove_dists", "outputs": {"logfile": {"src": "hda", "id": "0e8331efcfcf7646", "uuid": "ef7d16e8-1735-4873-871a-3b2fe6866839"}, "pick_dist": {"src": "hda", "id": "8221ac349ab6487f", "uuid": "102ef663-b92e-438f-a2ee-b654258fb954"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.dists(accnos=accnos.dat,phylip=input_dist.dat)\nRemoved 8 groups or sequences from your phylip file.\n\nOutput File names: \ninput_dist.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2283.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2282.dat' input_dist.dat &&  echo 'remove.dists( accnos=accnos.dat, phylip=input_dist.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:13:45.005251", "params": {"input": "{\"source\": \"phylip\", \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 2282}]}, \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31491", "id": "9fbd2c401152ab55", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_dists.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"groupnames|groups": "pasture", "groupnames|shared_in": {"src": "hda", "id": "7cd2d53bde5c0add"}, "groupnames|source": "shared"}, "job": {"inputs": {"shared_in": {"src": "hda", "id": "7cd2d53bde5c0add", "uuid": "9fc9bf7a-54c3-46a7-98c1-6c34d55e6493"}}, "update_time": "2018-02-08T18:14:07.678472", "tool_id": "mothur_remove_groups", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "6b7768dc0d7faad7", "uuid": "52eaf5c0-1c63-4c6c-810a-cb578e07f35c"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "f0a5105eaf2bfd75", "uuid": "6326cda0-94d7-4c15-9dfd-4564c1d99e95"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "9189bcfe7a4f9acb", "uuid": "850ecac9-5693-424b-b406-cc0f7ec2dbd1"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "95a9440ff1992c74", "uuid": "c6690a15-1f6d-4594-9281-42266a8f206b"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "bc85128d647d7567", "uuid": "290c9a03-ddb4-436d-b2b5-007a67af45da"}, "__new_primary_file_unique|0.16__": {"src": "hda", "id": "945066983ff522f4", "uuid": "d13a6213-50bb-4fb7-a41e-1adfe97db47f"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "76b454b70e887011", "uuid": "04ea0f09-ff28-48db-80d1-c2ecbe35cd9d"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "1eb9c4a1b6283f8b", "uuid": "7a142fbc-2114-4cb3-8d6b-8b1662076b6f"}, "__new_primary_file_unique|0.15__": {"src": "hda", "id": "119e335ad3ed5286", "uuid": "9d58df98-0918-427b-a6ed-16ff74b4c563"}, "__new_primary_file_unique|0.08__": {"src": "hda", "id": "098d7fe116d7a465", "uuid": "c6aea6dc-234c-4eb4-b5a5-00d80e49e5ea"}, "__new_primary_file_unique|0.14__": {"src": "hda", "id": "9dc99095cef129ee", "uuid": "4a584369-937c-4a50-bac2-715c486f0cbd"}, "__new_primary_file_unique|0.13__": {"src": "hda", "id": "222b3bca2d12ce45", "uuid": "e1d76e2c-74b5-46fa-b24d-8ce47e3fed27"}, "__new_primary_file_unique|0.09__": {"src": "hda", "id": "f35d48acb5b4927b", "uuid": "b459fadf-aec6-426d-9592-e6469bdac959"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "4db0932fb7553ad2", "uuid": "508d6ab7-f650-4b40-865b-7f944c0d7708"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "ad125357e7c3e87b", "uuid": "ce80010f-02b5-4a66-b4c3-5d503159c131"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "cb25081baf7393e6", "uuid": "1b5c8138-1926-4860-a8dc-3faf16fc08c9"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "6f03d3200088c6d4", "uuid": "688d58fe-be06-4732-a939-5c6383d2ff38"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "50d24fe68016bea8", "uuid": "1b876dae-ba70-4e10-99f2-cb0bd6bda909"}, "__new_primary_file_unique|0.25__": {"src": "hda", "id": "17e5da6fef26fa49", "uuid": "fb0545f6-73e3-4eaa-8f8f-eac7226ac969"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "7e316548162b36ff", "uuid": "8c561f2b-f96b-44cd-81c4-2e5ba77246ff"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "6a9f3b4b5ee84850", "uuid": "9f5a2c4c-b778-474a-b1aa-3a8f5c82de76"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "da24b85de09d096b", "uuid": "13bf9e55-cb11-49e9-8bef-b0ac93f6a05e"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "592e977e25982094", "uuid": "95e8440a-a46e-4c30-b120-6dddf2132d0a"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "c3a2d976a363681a", "uuid": "c1037b1f-37f6-4cd7-853f-495eecdfbfca"}, "logfile": {"src": "hda", "id": "f484cc634deaf2d7", "uuid": "af4651b4-a073-4a02-a828-c9e80e42f9c4"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "fae2800d127612ca", "uuid": "4e3bf2cb-1e57-4555-8a88-a70f3d3fff6c"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "f216775375f843a9", "uuid": "303ab49e-cd2e-4a82-8f79-380437279aed"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "809583a7f7d24a94", "uuid": "d500d714-fbe9-4eb4-8530-d30a30c828e2"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "953bda5fbdb92d27", "uuid": "cc738eb5-12eb-4492-bda6-95eae883806e"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "52627054db660e78", "uuid": "72f56beb-88be-42ae-a8aa-a637feee5026"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "e25f46671ff63694", "uuid": "6338dc42-8971-412c-8476-0a4e1319c4cb"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "d92cab7da43877a2", "uuid": "e5d9fc6a-5d11-471d-99cf-8526c01ae1b0"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "a8c47f290140529a", "uuid": "31b6efd0-20f9-4205-9da4-896acd31f0a3"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "12ab43a2c559fd70", "uuid": "2429c020-1da4-4394-984a-1e7fc01753ab"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "cc13e7b5b3a20008", "uuid": "f0e71ae2-2903-4585-a382-41a731ff0ed7"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "39ce81f662090b83", "uuid": "00450dbd-ee23-4fc9-b219-2e25eebb3ea9"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "64ce508563105809", "uuid": "ad7ab1f7-8c29-4ff8-bd3c-d4943f4549e4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.groups(shared=groupnames_shared_in.dat,groups=pasture)\nRemoved groups: pasture from your shared file.\n\nOutput File names: \ngroupnames_shared_in.unique.pick.dat\ngroupnames_shared_in.0.01.pick.dat\ngroupnames_shared_in.0.02.pick.dat\ngroupnames_shared_in.0.03.pick.dat\ngroupnames_shared_in.0.04.pick.dat\ngroupnames_shared_in.0.05.pick.dat\ngroupnames_shared_in.0.06.pick.dat\ngroupnames_shared_in.0.07.pick.dat\ngroupnames_shared_in.0.08.pick.dat\ngroupnames_shared_in.0.09.pick.dat\ngroupnames_shared_in.0.10.pick.dat\ngroupnames_shared_in.0.11.pick.dat\ngroupnames_shared_in.0.12.pick.dat\ngroupnames_shared_in.0.13.pick.dat\ngroupnames_shared_in.0.14.pick.dat\ngroupnames_shared_in.0.15.pick.dat\ngroupnames_shared_in.0.16.pick.dat\ngroupnames_shared_in.0.17.pick.dat\ngroupnames_shared_in.0.18.pick.dat\ngroupnames_shared_in.0.19.pick.dat\ngroupnames_shared_in.0.20.pick.dat\ngroupnames_shared_in.0.21.pick.dat\ngroupnames_shared_in.0.22.pick.dat\ngroupnames_shared_in.0.23.pick.dat\ngroupnames_shared_in.0.24.pick.dat\ngroupnames_shared_in.0.25.pick.dat\ngroupnames_shared_in.0.26.pick.dat\ngroupnames_shared_in.0.27.pick.dat\ngroupnames_shared_in.0.29.pick.dat\ngroupnames_shared_in.0.32.pick.dat\ngroupnames_shared_in.0.33.pick.dat\ngroupnames_shared_in.0.36.pick.dat\ngroupnames_shared_in.0.38.pick.dat\ngroupnames_shared_in.0.41.pick.dat\ngroupnames_shared_in.0.45.pick.dat\ngroupnames_shared_in.0.55.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2286.dat' groupnames_shared_in.dat &&  echo 'remove.groups( shared=groupnames_shared_in.dat ,groups=pasture )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:14:02.554551", "params": {"groupnames": "{\"source\": \"shared\", \"shared_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2286}]}, \"groups\": \"pasture\", \"__current_case__\": 1}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31584", "id": "11f90d7d2e7018d3", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_groups.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"groupnames|fasta_in": {"src": "hda", "id": "834c7bc81907531a"}, "groupnames|group_in": {"src": "hda", "id": "1ae0e921e8a5c2cf"}, "groupnames|list_in": {"src": "hda", "id": "2dddc34ce42fd89f"}, "groupnames|name_in": {"src": "hda", "id": "511d67f899681d88"}, "groupnames|source": "other", "groupnames|taxonomy_in": {"src": "hda", "id": "a0efceb0cae627df"}, "groupnames|groups": "pasture"}, "job": {"inputs": {"group_in": {"src": "hda", "id": "1ae0e921e8a5c2cf", "uuid": "5f2e2590-4c79-43f0-af0d-25436dd84f90"}, "taxonomy_in": {"src": "hda", "id": "a0efceb0cae627df", "uuid": "f179b10b-16a7-477b-9295-fedc1fc19a3f"}, "fasta_in": {"src": "hda", "id": "834c7bc81907531a", "uuid": "f554b893-67c6-4207-93ab-bf2fac70ed15"}, "list_in": {"src": "hda", "id": "2dddc34ce42fd89f", "uuid": "4f3dd394-cf1f-438a-b333-4d7e02f5ba59"}, "name_in": {"src": "hda", "id": "511d67f899681d88", "uuid": "3b977018-74eb-4b17-aa0e-3b8200e38105"}}, "update_time": "2018-02-08T18:14:44.254800", "tool_id": "mothur_remove_groups", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "538d841fdb1747d9", "uuid": "7f614d2c-59f1-4934-951a-e7b3ac38e607"}, "fasta_out": {"src": "hda", "id": "379ef8aadc41efc2", "uuid": "bc8b8938-fbd1-45c2-8106-20e561e90f55"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "fd811d57601c2a53", "uuid": "94cc848c-3ced-47cd-b630-9d388be1b6d3"}, "name_out": {"src": "hda", "id": "a57ffcdbbf6f1e3c", "uuid": "751e63d8-425f-457a-96c7-8d7e2cc79bea"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "7b968d941cfc816e", "uuid": "abaccccb-c543-4076-bbb1-4d9b11dad510"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "a279471fedaa0571", "uuid": "5f667714-7be9-49db-bc3c-ab67b2d8f34b"}, "__new_primary_file_unique|0.16__": {"src": 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{"src": "hda", "id": "d953aaed8dbb68b6", "uuid": "4b9236a6-d383-46ff-93d2-a13205f630c6"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "2901353778bc9bab", "uuid": "1929f6b3-459f-4ff3-aeba-09eac2503eb0"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "c2b20c6dcfa71d17", "uuid": "da641b6f-a6a5-4b4a-9df9-efe6bd1eeb43"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "22914d39b2b730a1", "uuid": "70abbaed-7677-4355-9afa-233bc72baff7"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "fe166579c3479639", "uuid": "73748fc9-5352-4ec9-8bce-2a4e9cbf49d7"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "919fc57758c35349", "uuid": "524cfd5b-5f80-44d2-8be5-5a1b2c1880db"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "47d62a7ea7c59a47", "uuid": "7929d82e-e335-4c1a-8f1c-bdc0a0a23663"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "d17e43f40c7b280e", "uuid": "f39b4998-1885-4a4c-afb2-ad9298c89c28"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "5ab0e040a82c9257", "uuid": "27a0e294-4ef3-45fe-addd-d866f364c10a"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "e7a119cd3c5740ed", "uuid": "886c83f7-6f69-4f10-bbce-8fa934177fb4"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "587a4a63fe83b80d", "uuid": "aec15976-5eec-40b3-b4fd-e8edb832801c"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "9e190863641df143", "uuid": "e7d3492c-0143-46ae-a44b-7c0e49ab3524"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "ff3f7fa6cf2588ee", "uuid": "b5f79860-46c3-4b66-a3cf-6e6c8398339f"}, "logfile": {"src": "hda", "id": "295945eae8ee0845", "uuid": "2e1d3528-177d-4161-940d-bbf57f0ffc3c"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "91547bc6b52d15e0", "uuid": "81da8bf2-74a2-4d6f-92d5-5bb64e320e9e"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "2b2e28ff432ff04c", "uuid": "53bea491-e5a0-4808-895f-74df32c455f1"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "2783f52461a8e0f8", "uuid": "4f01b970-6761-478c-8f83-76482de991d0"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "25a6596e48ff11f8", "uuid": "9ca8c213-cedc-4d59-91a9-e8135c64adad"}, "group_out": {"src": "hda", "id": "44f8738bed3b883e", "uuid": "f7ebf868-97b1-475a-a1f7-14cc02aa2f0b"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "c2205b1bae1af899", "uuid": "4292a3b8-6edc-47b6-92d9-97eb03bd0c44"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "704100c2f064b409", "uuid": "1df841f9-0466-435b-96b0-9e7122a8c05f"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "052e581adee82db7", "uuid": "e6f5cd12-1eb1-44fb-b452-76fe29d57671"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "be2f9646583e3df7", "uuid": "e4692991-1e4f-4595-a46e-14c689b6ff47"}, "taxonomy_out": {"src": "hda", "id": "9baff05b3688be9e", "uuid": "ecc211a5-1969-4669-a4d2-6534670051c1"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "890f24b7838786dd", "uuid": "c84f631a-8807-474b-8723-5609c8d5b552"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "decd1f544b8f4602", "uuid": "6d116afa-e9ac-48f9-9835-4ee3691cf677"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "99bfead4bdf5ed3d", "uuid": "a00cdfde-cec4-45b5-9e69-c9ee754ff2a5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.groups(group=groupnames_group_in.dat,fasta=groupnames_fasta_in.d \rat,name=groupnames_name_in.dat,list=groupnames_list_in.dat,taxonomy=groupnames_t \raxonomy_in.dat,groups=pasture)\nRemoved 49 sequences from your name file.\nRemoved 49 sequences from your fasta file.\nRemoved 49 sequences from your group file.\nRemoved 49 sequences from your list file.\nRemoved 49 sequences from your taxonomy file.\n\nOutput File names: \ngroupnames_name_in.pick.dat\ngroupnames_fasta_in.pick.dat\ngroupnames_group_in.pick.dat\ngroupnames_list_in.unique.pick.dat\ngroupnames_list_in.0.01.pick.dat\ngroupnames_list_in.0.02.pick.dat\ngroupnames_list_in.0.03.pick.dat\ngroupnames_list_in.0.04.pick.dat\ngroupnames_list_in.0.05.pick.dat\ngroupnames_list_in.0.06.pick.dat\ngroupnames_list_in.0.07.pick.dat\ngroupnames_list_in.0.08.pick.dat\ngroupnames_list_in.0.09.pick.dat\ngroupnames_list_in.0.10.pick.dat\ngroupnames_list_in.0.11.pick.dat\ngroupnames_list_in.0.12.pick.dat\ngroupnames_list_in.0.13.pick.dat\ngroupnames_list_in.0.14.pick.dat\ngroupnames_list_in.0.15.pick.dat\ngroupnames_list_in.0.16.pick.dat\ngroupnames_list_in.0.17.pick.dat\ngroupnames_list_in.0.18.pick.dat\ngroupnames_list_in.0.19.pick.dat\ngroupnames_list_in.0.20.pick.dat\ngroupnames_list_in.0.21.pick.dat\ngroupnames_list_in.0.22.pick.dat\ngroupnames_list_in.0.23.pick.dat\ngroupnames_list_in.0.24.pick.dat\ngroupnames_list_in.0.25.pick.dat\ngroupnames_list_in.0.26.pick.dat\ngroupnames_list_in.0.27.pick.dat\ngroupnames_list_in.0.29.pick.dat\ngroupnames_list_in.0.32.pick.dat\ngroupnames_list_in.0.33.pick.dat\ngroupnames_list_in.0.36.pick.dat\ngroupnames_list_in.0.38.pick.dat\ngroupnames_list_in.0.41.pick.dat\ngroupnames_list_in.0.45.pick.dat\ngroupnames_list_in.0.55.pick.dat\ngroupnames_taxonomy_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2324.dat' groupnames_group_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2325.dat' groupnames_fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2326.dat' groupnames_name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2327.dat' groupnames_list_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2328.dat' groupnames_taxonomy_in.dat &&  echo 'remove.groups( group=groupnames_group_in.dat ,fasta=groupnames_fasta_in.dat ,name=groupnames_name_in.dat ,list=groupnames_list_in.dat ,taxonomy=groupnames_taxonomy_in.dat ,groups=pasture )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:14:37.618375", "params": {"groupnames": "{\"__current_case__\": 0, \"group_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2324}]}, \"fasta_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2325}]}, \"source\": \"other\", \"taxonomy_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2328}]}, \"groups\": \"pasture\", \"list_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2327}]}, \"name_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2326}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31756", "id": "6dd0e474af427e2d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_groups.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "b4b60426d425f16d"}, "file|taxonomy": {"src": "hda", "id": "37986503f50eefa5"}, "file|filetype": "usetaxonomy", "taxon": "Bacteria;Firmicutes;"}, "job": {"inputs": {"count": {"src": "hda", "id": "b4b60426d425f16d", "uuid": "d3102d63-f063-4f49-9358-a9204932afa5"}, "taxonomy": {"src": "hda", "id": "37986503f50eefa5", "uuid": "d3943489-f9bc-4e8f-b7fa-47058d56089a"}}, "update_time": "2018-02-08T18:15:26.271587", "tool_id": "mothur_remove_lineage", "outputs": {"logfile": {"src": "hda", "id": "f1a6b922e4c3946b", "uuid": "614bb54e-30c0-4890-aec7-0081dbee7bdf"}, "taxonomy_out": {"src": "hda", "id": "4b38cb8245b4e765", "uuid": "a9ddb677-1dab-4ebf-9e68-e8ea6af15451"}, "count_out": {"src": "hda", "id": "0160af6439ac70dc", "uuid": "14df1388-869a-42d5-a461-262f0dca79ac"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.lineage(taxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;', \rcount=count.dat)\n\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n\nOutput File Names: \nfile.taxonomy.pick.dat\ncount.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2370.dat' file.taxonomy.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2371.dat' count.dat &&  echo 'remove.lineage( taxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;'\"' ,count=count.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:15:23.028671", "params": {"dups": "\"true\"", "fasta_in": "null", "taxon": "\"Bacteria;Firmicutes;\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 2370}]}, \"filetype\": \"usetaxonomy\", \"taxons\": null, \"__current_case__\": 0}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "31874", "id": "0988466323c56cdf", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_lineage.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta_in": {"src": "hda", "id": "94ffe1907bbe589a"}, "taxon": "Bacteria;Firmicutes;,Bacteria;Actinobacteria;", "list_in": {"src": "hda", "id": "a9cef69b5a19731f"}, "group_in": {"src": "hda", "id": "ca154bf63cdc8557"}, "file|taxonomy": {"src": "hda", "id": "7b13643ca1c390d8"}, "alignreport_in": {"src": "hda", "id": "e3e164d6ab182280"}, "file|filetype": "usetaxonomy", "name_in": {"src": "hda", "id": "4cc77546f573b2d0"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "7b13643ca1c390d8", "uuid": "a450e3b8-6804-43fe-823a-9cb57a712356"}, "fasta_in": {"src": "hda", "id": "94ffe1907bbe589a", "uuid": "fe69accc-1298-42f3-bfe2-28a855239d6f"}, "group_in": {"src": "hda", "id": "ca154bf63cdc8557", "uuid": "dbc42af8-2faa-4e02-bb57-5a7217ecb809"}, "alignreport_in": {"src": "hda", "id": "e3e164d6ab182280", "uuid": "d78e1f6e-58b5-425c-9670-14708fcb21e3"}, "list_in": {"src": "hda", "id": "a9cef69b5a19731f", "uuid": "92e9416c-6784-438f-b095-94328935f7ea"}, "name_in": {"src": "hda", "id": "4cc77546f573b2d0", "uuid": "96af4f9b-9c52-4b47-a5e3-3cde1fbb8fd7"}}, "update_time": "2018-02-08T18:15:53.229707", "tool_id": "mothur_remove_lineage", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "35df3e45f29e684d", "uuid": "b57fd9af-0c5a-49d5-81a2-d949025c7d33"}, "fasta_out": {"src": "hda", "id": "154b33b739461382", "uuid": "f99759ef-0ea0-4bc2-b49b-6b3d962f7ad7"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "39ac9d7d68a18ba7", "uuid": "060bf7ce-0b28-42c1-9f72-d46a07a677a3"}, "name_out": {"src": "hda", "id": "966910197fb6271c", "uuid": "3a77e387-fe91-4e61-a86b-067989473500"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "1fe329e39785826e", "uuid": "34ed1f23-984d-4ebe-b793-8ff8f4b4078b"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "7ba9e4d18c68940c", "uuid": "dfb2a6e1-e8a9-40b2-b831-1de06f934a1a"}, "__new_primary_file_unique|0.16__": {"src": "hda", "id": "7b6cf8e7ca9d489b", "uuid": "aeb38b27-2272-4bd6-bc16-88f8b16e8a70"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "ebb161f2aaac9134", "uuid": "e38efc93-7800-498b-b7e3-daff6a00ad43"}, "__new_primary_file_unique|0.25__": {"src": "hda", "id": "892ed2ca0d452bf1", "uuid": "76067942-5b7d-4cdf-b3f3-cc476a170d56"}, "__new_primary_file_unique|0.15__": {"src": "hda", "id": "32d3c44266e502db", "uuid": "1d7490a3-4f7c-425c-b1dc-598b22db89d0"}, "__new_primary_file_unique|0.08__": {"src": "hda", "id": "e7f38b62472c64c3", "uuid": "4e8c6090-0995-43f9-abe3-5533dd48c1c6"}, "__new_primary_file_unique|0.14__": {"src": "hda", "id": "54362bd1402420de", "uuid": "18d2356b-d07a-4cae-ba0d-4a99c5999d54"}, "__new_primary_file_unique|0.13__": {"src": "hda", "id": "dd9637d99eee3c9a", "uuid": "bf35fdfc-f9c8-4abe-b5d1-a5404ba227cc"}, "__new_primary_file_unique|0.09__": {"src": "hda", "id": "2b2a8e7a960a22fa", "uuid": "381b3d66-aad2-4fe1-aba6-848f29164cbd"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "9a4998a57b4c0d76", "uuid": "83125373-a266-410f-9eb1-aed2d893afcc"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "805aa78c406b7f16", "uuid": "63e6ba39-b3bb-42d5-a22c-7441eae9c452"}, "alignreport_out": {"src": "hda", "id": "8b80c2f064b944ad", "uuid": "f543a295-d0c4-4100-8a54-5167862c3d7f"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "681ee48f048bfa32", "uuid": "64896760-acab-4742-ae43-ae02551402b0"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "5f7b03e27cadea29", "uuid": "9cc904d5-e08c-42d4-81bd-af5283278209"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "67254bb77b4cd837", "uuid": "47a70053-ca58-4d60-a0d1-7ce682cb2e03"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "c00f338d3be3421b", "uuid": "62c8c379-dcde-493c-bc3c-627e6469a663"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "4e2a688e84ed09ba", "uuid": "aa045ae7-fa22-4063-9da8-3e0b2b849fe8"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "e8e6125857b80021", "uuid": "4dc4da63-a755-4292-85bc-d9c7d538a032"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "edc838c8e1dee637", "uuid": "6d3bc26f-2de4-479d-b5db-5523f5ed1937"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "077990f262b60a5e", "uuid": "92ea14ba-6c77-4a9c-90d9-0cde541beeef"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "3151b1fe3738d9ad", "uuid": "e34e5a1a-5a77-48f2-9607-38ceaed666f3"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "cd0552060d28d57c", "uuid": "3cb838e3-dff0-44c6-842d-2859ecfb8326"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "9199779695f12b0d", "uuid": "bbd54f24-af02-462a-89a9-380299425388"}, "logfile": {"src": "hda", "id": "044d4dd6116ec211", "uuid": "ca36d78c-50a7-4745-b419-dac4ee3cb648"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "8a3d90f0472ffba1", "uuid": "90a0f0da-db5e-4d53-a9f0-5f1ee8b7111a"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "328d2c0dfb26d583", "uuid": "a16b25ca-5454-4a53-bfdd-12d4fe134a16"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "ea46dea1984f7f15", "uuid": "dd3b45ae-817f-4044-8d1d-aa76c21c24bd"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "85823b54d11c9421", "uuid": "832e1bc0-6570-4cde-a8ad-113d43ccccd1"}, "group_out": {"src": "hda", "id": "68a1cd10847ef2c7", "uuid": "dde1184e-4e0d-4082-879d-a1052559ad20"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "e2c9e714bcfe5f0a", "uuid": "4bd958da-db4b-4ada-9df6-819d8789a400"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "0f9e12470eed7630", "uuid": "13073578-c0ce-489f-9b51-d681adf6ebfb"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "3070aa5bf5842a22", "uuid": "7843242e-b223-419f-88a1-78a98232840e"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "1f2d20dc0bea074f", "uuid": "d330650b-bd3e-42d0-ab00-744aa59e3ea3"}, "taxonomy_out": {"src": "hda", "id": "f515de207b3cbff0", "uuid": "3ed1f17c-9b2e-466d-8d52-761b4c550138"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "77b0f6eda081c1d2", "uuid": "35f92abe-1f92-4ded-a945-494da0e27cab"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "ef503f389d24c62c", "uuid": "385b5438-9c5f-4d4e-bfb3-7c89bc0da895"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "4a0f32fd437d1f2f", "uuid": "597c450c-319f-4fb0-a221-f8bc15ed16b1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.lineage(taxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;-B \racteria;Actinobacteria;',fasta=fasta_in.dat,group=group_in.dat,alignreport=align \rreport_in.dat,list=list_in.dat,name=name_in.dat,dups=true)\nYou did not provide a label, I will use the first label in your inputfile.\n\nOutput File Names: \nfile.taxonomy.pick.dat\nname_in.pick.dat\nfasta_in.pick.dat\ngroup_in.pick.dat\nalignreport_in.pick.align.report\nlist_in.unique.pick.dat\nlist_in.0.01.pick.dat\nlist_in.0.02.pick.dat\nlist_in.0.03.pick.dat\nlist_in.0.04.pick.dat\nlist_in.0.05.pick.dat\nlist_in.0.06.pick.dat\nlist_in.0.07.pick.dat\nlist_in.0.08.pick.dat\nlist_in.0.09.pick.dat\nlist_in.0.10.pick.dat\nlist_in.0.11.pick.dat\nlist_in.0.12.pick.dat\nlist_in.0.13.pick.dat\nlist_in.0.14.pick.dat\nlist_in.0.15.pick.dat\nlist_in.0.16.pick.dat\nlist_in.0.17.pick.dat\nlist_in.0.18.pick.dat\nlist_in.0.19.pick.dat\nlist_in.0.20.pick.dat\nlist_in.0.21.pick.dat\nlist_in.0.22.pick.dat\nlist_in.0.23.pick.dat\nlist_in.0.24.pick.dat\nlist_in.0.25.pick.dat\nlist_in.0.26.pick.dat\nlist_in.0.27.pick.dat\nlist_in.0.29.pick.dat\nlist_in.0.32.pick.dat\nlist_in.0.33.pick.dat\nlist_in.0.36.pick.dat\nlist_in.0.38.pick.dat\nlist_in.0.41.pick.dat\nlist_in.0.45.pick.dat\nlist_in.0.55.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2375.dat' file.taxonomy.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2376.dat' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2377.dat' group_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2378.dat' alignreport_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2379.dat' list_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2380.dat' name_in.dat && ln -s 'None' count.dat &&  echo 'remove.lineage( taxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;-Bacteria;Actinobacteria;'\"' ,fasta=fasta_in.dat ,group=group_in.dat ,alignreport=alignreport_in.dat ,list=list_in.dat ,name=name_in.dat ,dups=true )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:15:46.002408", "params": {"count": "null", "dups": "\"true\"", "taxon": "\"Bacteria;Firmicutes;,Bacteria;Actinobacteria;\"", "dbkey": "\"hg17\"", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 2375}]}, \"filetype\": \"usetaxonomy\", \"taxons\": null, \"__current_case__\": 0}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32079", "id": "028963dd9277afc4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_lineage.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"file|taxonomy": {"src": "hda", "id": "ed2d3bd032d02491"}, "file|taxons": ["Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Dorea(99);", "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(47);"], "file|filetype": "usetaxonomy"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "ed2d3bd032d02491", "uuid": "d644aec4-7267-44fd-b5df-fb5e984e6a7b"}}, "update_time": "2018-02-08T18:16:32.338513", "tool_id": "mothur_remove_lineage", "outputs": {"logfile": {"src": "hda", "id": "9e8cf296dbef59b9", "uuid": "0de51807-6b53-4167-bffb-0e6be06a2fbe"}, "taxonomy_out": {"src": "hda", "id": "747c6fc35e775aa4", "uuid": "479efb57-7437-4758-995d-c2fce07b43e5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.lineage(taxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicutes;Cl \rostridia;Clostridiales;Lachnospiraceae;Dorea;-Bacteria;Firmicutes;Clostridia;Clo \rstridiales;Lachnospiraceae;Roseburia;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2423.dat' file.taxonomy.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat &&  echo 'remove.lineage( taxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Dorea;-Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Roseburia;'\"' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:16:29.164896", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 2423}]}, \"filetype\": \"usetaxonomy\", \"taxons\": [\"Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Dorea(99);\", \"Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(47);\"], \"__current_case__\": 0}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32183", "id": "f941dab79996470b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_lineage.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"file|taxonomy": {"src": "hda", "id": "b1deaf4adb6e2b62"}, "file|filetype": "useconstaxonomy", "taxon": "Bacteria;Bacteroidetes;"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "b1deaf4adb6e2b62", "uuid": "cad89d39-f18f-47c7-ae46-976e6995b23b"}}, "update_time": "2018-02-08T18:16:39.822280", "tool_id": "mothur_remove_lineage", "outputs": {"logfile": {"src": "hda", "id": "990b9da175c7f56f", "uuid": "13e9c57b-ff63-4da7-8cdb-a84d5c2374f1"}, "taxonomy_out": {"src": "hda", "id": "b879287775e7651a", "uuid": "510e5454-dc71-430a-a471-c8d98b2623ee"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.lineage(constaxonomy=file.taxonomy.dat,taxon='Bacteria;Bacteroid \retes;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2426.dat' file.taxonomy.dat && ln -s 'None' file.shared.dat && ln -s 'None' file.list.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat &&  echo 'remove.lineage( constaxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Bacteroidetes;'\"' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:16:36.478165", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"Bacteria;Bacteroidetes;\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 2426}]}, \"filetype\": \"useconstaxonomy\", \"list\": null, \"taxons\": null, \"__current_case__\": 1, \"shared\": null}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32280", "id": "3b489b444bd4d351", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_lineage.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"file|taxonomy": {"src": "hda", "id": "f493e0cacca6ba40"}, "file|taxons": ["Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;", "Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;"], "file|filetype": "useconstaxonomy"}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "f493e0cacca6ba40", "uuid": "0c8ec11a-5b60-494d-a66c-7e9e51c46569"}}, "update_time": "2018-02-08T18:16:46.831147", "tool_id": "mothur_remove_lineage", "outputs": {"logfile": {"src": "hda", "id": "6b6553db05727bc4", "uuid": "0cbf6caf-ee62-40c3-bc5c-89bb32db7ab4"}, "taxonomy_out": {"src": "hda", "id": "42de286dcd9bca3b", "uuid": "560bd4aa-7924-4454-acf6-5f4f0b173c55"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.lineage(constaxonomy=file.taxonomy.dat,taxon='Bacteria;Firmicute \rs;Clostridia;Clostridiales;Lachnospiraceae;unclassified;-Bacteria;Proteobacteria \r;Gammaproteobacteria;unclassified;unclassified;unclassified;')\n\nOutput File Names: \nfile.taxonomy.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2429.dat' file.taxonomy.dat && ln -s 'None' file.shared.dat && ln -s 'None' file.list.dat && ln -s 'None' fasta_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat &&  echo 'remove.lineage( constaxonomy=file.taxonomy.dat ,taxon='\"'Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;unclassified;-Bacteria;Proteobacteria;Gammaproteobacteria;unclassified;unclassified;unclassified;'\"' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:16:43.668260", "params": {"count": "null", "dups": "\"true\"", "fasta_in": "null", "taxon": "\"\"", "dbkey": "\"hg17\"", "group_in": "null", "file": "{\"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 2429}]}, \"filetype\": \"useconstaxonomy\", \"list\": null, \"taxons\": [\"Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;\", \"Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;\"], \"__current_case__\": 1, \"shared\": null}", "alignreport_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32375", "id": "ee234bf95ca1c311", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_lineage.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"infile|label": "0.22", "accnos": {"src": "hda", "id": "ad5a23682f5a9de8"}, "infile|otu": {"src": "hda", "id": "60c41917f147cedf"}, "infile|intype": "in_shared"}, "job": {"inputs": {"accnos": {"src": "hda", "id": "ad5a23682f5a9de8", "uuid": "dfb149e3-265e-4981-a24f-f7c07789024f"}, "otu": {"src": "hda", "id": "60c41917f147cedf", "uuid": "246499f3-daf4-40f1-87b5-e811cadaafb8"}}, "update_time": "2018-02-08T18:16:58.146683", "tool_id": "mothur_remove_otulabels", "outputs": {"pick_out": {"src": "hda", "id": "e1054de073a99e69", "uuid": "b49a638e-3568-4829-9fd0-3ff32e10f5a9"}, "logfile": {"src": "hda", "id": "47efcc304726fc94", "uuid": "fd34616d-4328-4264-a888-df65224a1559"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.otulabels(list=infile.otu.dat,label=0.22,accnos=accnos.dat)\nRemoved 0 OTUs from your list file.\n\nOutput File Names: \ninfile.otu.0.22.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2433.dat' infile.otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2432.dat' accnos.dat &&  echo 'remove.otulabels( list=infile.otu.dat, label=0.22, accnos=accnos.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:16:54.307572", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2433}]}, \"__current_case__\": 0, \"label\": \"0.22\"}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32499", "id": "211650f16125cac7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_otulabels.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"infile|intype": "in_other", "accnos": {"src": "hda", "id": "b96a437033ff865d"}, "infile|otu": {"src": "hda", "id": "ad0fe0deb4088e0a"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "b96a437033ff865d", "uuid": "293f7fdd-29e5-4ec3-a842-6d2ac7e20f8a"}, "otu": {"src": "hda", "id": "ad0fe0deb4088e0a", "uuid": "e25e2bb1-a988-4495-aa5b-ae2109332f27"}}, "update_time": "2018-02-08T18:17:20.896014", "tool_id": "mothur_remove_otulabels", "outputs": {"pick_out": {"src": "hda", "id": "a18ae6974f6e6e5c", "uuid": "37fe3947-e0a5-4943-95f3-ced1916d0ef5"}, "logfile": {"src": "hda", "id": "dd40e5394130ccc4", "uuid": "3f7cb677-9d83-41cb-95fd-dd0ab28b6842"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.otulabels(corraxes=infile.otu.dat,accnos=accnos.dat)\nRemoved 3 lines from your corr.axes file.\n\nOutput File Names: \ninfile.otu.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2437.dat' infile.otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2436.dat' accnos.dat &&  echo 'remove.otulabels( corraxes=infile.otu.dat, accnos=accnos.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:17:17.819966", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_other\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2437}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32611", "id": "a9fd5735f9e9e011", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_otulabels.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"infile|label": "0.22", "accnos": {"src": "hda", "id": "dee9a2b956d615f3"}, "infile|otu": {"src": "hda", "id": "95a921a378370eb3"}, "infile|intype": "in_shared"}, "job": {"inputs": {"accnos": {"src": "hda", "id": "dee9a2b956d615f3", "uuid": "f312c82b-dd3e-4742-83b1-faa00ea52c47"}, "otu": {"src": "hda", "id": "95a921a378370eb3", "uuid": "d50ce77c-745b-4796-ad7c-97e06777ede2"}}, "update_time": "2018-02-08T18:17:42.585808", "tool_id": "mothur_remove_otus", "outputs": {"pick_out": {"src": "hda", "id": "a4a23a6f4654f48d", "uuid": "b69b56ee-6910-484f-8878-451c53a57842"}, "logfile": {"src": "hda", "id": "4dc446e75a5ecd3d", "uuid": "0b525a00-65a9-4875-8492-68c94c2daca8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.otus(list=infile.otu.dat,label=0.22,accnos=accnos.dat)\nRemoved 0 OTUs from your list file.\n\nOutput File Names: \ninfile.otu.0.22.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2441.dat' infile.otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2440.dat' accnos.dat &&  echo 'remove.otus( list=infile.otu.dat, label=0.22, accnos=accnos.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:17:39.474122", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_shared\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2441}]}, \"__current_case__\": 0, \"label\": \"0.22\"}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "32731", "id": "e70b3a347edd9ca6", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_otus.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"infile|intype": "in_other", "accnos": {"src": "hda", "id": "cbb415d7495a9afc"}, "infile|otu": {"src": "hda", "id": "0f3352b51fa58ea1"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "cbb415d7495a9afc", "uuid": "22ef75e5-ca16-490c-86c4-86c8bdbced41"}, "otu": {"src": "hda", "id": "0f3352b51fa58ea1", "uuid": "5c49889c-5afb-4d18-92ef-1687076479eb"}}, "update_time": "2018-02-08T18:18:04.247034", "tool_id": "mothur_remove_otus", "outputs": {"pick_out": {"src": "hda", "id": "d3b44446654bd5f7", "uuid": "0e55b880-120c-401d-9d78-43466eef7469"}, "logfile": {"src": "hda", "id": "d02a20be41406d2e", "uuid": "92f22a11-d731-4b0c-8019-a7d9c3c48f30"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.otus(corraxes=infile.otu.dat,accnos=accnos.dat)\nRemoved 3 lines from your corr.axes file.\n\nOutput File Names: \ninfile.otu.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2445.dat' infile.otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2444.dat' accnos.dat &&  echo 'remove.otus( corraxes=infile.otu.dat, accnos=accnos.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:18:01.130590", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "infile": "{\"intype\": \"in_other\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2445}]}, \"__current_case__\": 1}", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "388", "id": "8325c15a45021320", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_otus.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input|source": "list", "input|otu": {"src": "hda", "id": "34aad423ffafab1b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "34aad423ffafab1b", "uuid": "a955bc96-7ca4-432c-8d66-f8e2731f1fa0"}}, "update_time": "2018-02-08T18:18:22.801087", "tool_id": "mothur_remove_rare", "outputs": {"logfile": {"src": "hda", "id": "ee9b6579bd835e40", "uuid": "a8cfb161-0cb1-4361-9c10-788601368a8b"}, "pick_otu": {"src": "hda", "id": "3308e08d6eccd8a7", "uuid": "ba89e863-a3c4-4703-ab0b-6618e9e81f78"}, "pick_group": {"src": "hda", "id": "a29b3ee6f6fed501", "uuid": "0b84979c-17af-4795-a581-e282687e4a64"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.rare(list=input_otu.dat,nseqs=1)\nFor the listfile you must select one label, using first label in your listfile.\n\nOutput File Names: \ninput_otu.unique.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2448.dat' input_otu.dat && ln -s 'None' input.group.dat && ln -s 'None' input.count.dat &&  echo 'remove.rare( list=input_otu.dat, nseqs=1 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:18:18.940186", "params": {"input": "{\"count\": null, \"group\": null, \"__current_case__\": 1, \"label\": null, \"source\": \"list\", \"groups\": null, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2448}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "nseqs": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "477", "id": "0679f69ae9556809", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_rare.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input|group": {"src": "hda", "id": "c7eb5c5f4746140d"}, "input|source": "list", "input|groups": ["forest", "pasture"], "input|otu": {"src": "hda", "id": "d7b7068fa7538c88"}}, "job": {"inputs": {"group": {"src": "hda", "id": "c7eb5c5f4746140d", "uuid": "7388ff4a-b437-4cfa-ae76-3ab6cd2a951e"}, "otu": {"src": "hda", "id": "d7b7068fa7538c88", "uuid": "8e56acb5-b99b-4966-b64b-674a19c8b445"}}, "update_time": "2018-02-08T18:18:45.594415", "tool_id": "mothur_remove_rare", "outputs": {"logfile": {"src": "hda", "id": "157ddde73282f3fb", "uuid": "bf5722f6-f5ef-414a-a842-1a8a893ecacd"}, "pick_otu": {"src": "hda", "id": "1b495114166d9bc3", "uuid": "d31b64a5-9178-4114-abd7-8c2681c0b2fb"}, "pick_group": {"src": "hda", "id": "97bd1ba524aaaf3a", "uuid": "844bd5b6-89bf-48aa-8a92-14e9032a1358"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.rare(list=input_otu.dat,group=input.group.dat,groups=forest-past \rure,nseqs=1)\nFor the listfile you must select one label, using first label in your listfile.\n\nOutput File Names: \ninput.group.pick.dat\ninput_otu.unique.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2452.dat' input_otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2453.dat' input.group.dat && ln -s 'None' input.count.dat &&  echo 'remove.rare( list=input_otu.dat, group=input.group.dat, groups=forest-pasture, nseqs=1 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:18:42.385738", "params": {"input": "{\"count\": null, \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 2453}]}, \"__current_case__\": 1, \"label\": null, \"source\": \"list\", \"groups\": [\"forest\", \"pasture\"], \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2452}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "nseqs": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "599", "id": "2d4e92ce3c742824", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_rare.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input|source": "shared", "input|otu": {"src": "hda", "id": "3198a9da3f439604"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "3198a9da3f439604", "uuid": "9e9bb25b-8f5a-4777-a20a-e17460017e6f"}}, "update_time": "2018-02-08T18:19:10.034043", "tool_id": "mothur_remove_rare", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "610cd1f4e5b83a0c", "uuid": "6828233f-3774-4b20-8a93-6ab47ed28c1d"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "513d86575c74f7d0", "uuid": "f9b7f75c-4688-4b59-b99f-bf047b2ec04f"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "9baafa71c45079b3", "uuid": "bd5079b6-279a-4232-8469-33fafe2a5e66"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "e6f56cb50e173a01", "uuid": "f79063d9-0f95-450c-9704-955f89a2f8c5"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "700a0908817c405f", "uuid": "0f73604c-9a14-4e60-8896-aa61accb2fa7"}, "__new_primary_file_unique|0.16__": {"src": "hda", "id": "322c8a381eeeb501", "uuid": "eff8980f-266e-4894-9e3c-648428eb6315"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "119999e59bd419d5", "uuid": "1cb26251-b37c-4d10-bc69-be079c4bf5df"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "e26c7b8f9677aad0", "uuid": "0cc9c609-507b-4f2b-ba4b-a831a6c92145"}, "__new_primary_file_unique|0.15__": {"src": "hda", "id": "5d5adfb1fb49ce2c", "uuid": "cfbe6c7d-4028-48ba-b8c3-3ad5a5fc556f"}, "__new_primary_file_unique|0.08__": {"src": "hda", "id": "ab8e8b2bc0c15acd", "uuid": "ba4ed452-675e-40bc-987e-caa800a389f4"}, "__new_primary_file_unique|0.14__": {"src": "hda", "id": "8870c5f928bb333a", "uuid": "08d0a12a-e1ce-43be-9e09-6afd547c569e"}, "__new_primary_file_unique|0.13__": {"src": "hda", "id": "d07a38806b24d453", "uuid": "aff7864c-9ab8-4d0e-bf7b-b8bd02af4b92"}, "__new_primary_file_unique|0.09__": {"src": "hda", "id": "2297b690ab68e422", "uuid": "46827413-8dd3-43d1-a307-478eeb63c53e"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "31fece26dc8ce520", "uuid": "382f6308-a9b5-491b-98ee-3553f7ad604f"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "74e41b93abfa8004", "uuid": "68372d6c-15a2-43d8-9aa6-dae86d615854"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "10f3b133fbdfbf9f", "uuid": "4ef4f2fd-d729-4e2f-ba5e-d877b3f97900"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "636206ab34003c74", "uuid": "a450aefe-767d-44ee-b214-f8e1f6ffb340"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "0c81280a55e0de4e", "uuid": "2fefeb64-8dfb-4dab-940c-936c66ead31e"}, "__new_primary_file_unique|0.25__": {"src": "hda", "id": "d0db099eee1d29bc", "uuid": "d59104f8-497e-46df-ab6f-c4e1b6008c2c"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "ab61d935d8b06603", "uuid": "93f026c8-2811-4d2c-90fd-39a3a90dd51a"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "e9fd1bfe3c966ddd", "uuid": "1b03c3da-4e99-4f22-8ac8-dc7c37d60392"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "9fe5ee644c2e6c63", "uuid": "60848a9f-fb38-47c8-ba99-62021b1b7e5f"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "c1bb74450083f46e", "uuid": "966d2046-3229-46cc-bc92-71626bf97c3d"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "fea0057dfc409953", "uuid": "759d9426-cbca-45b2-8ddb-43e8f7b013af"}, "logfile": {"src": "hda", "id": "4f898abf2bba8db9", "uuid": "b89ade31-ba94-42d9-b11d-31bbaecbeed0"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "f8361ca1fe7540ad", "uuid": "fdb8b86e-5762-4aad-8c1e-b538c0d9b67a"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "51c08c22772eba1c", "uuid": "a71e3585-6b7a-4088-83e3-5498dc932ea6"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "056c262b45795646", "uuid": "7a782f58-afde-4af4-b59b-ab246348e1d9"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "f0439ffc253b657d", "uuid": "0624d10f-a3c2-4a2e-ab25-66276206798e"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "98e41e589857cd09", "uuid": "ae4ba94b-efb1-468a-86c2-bc6728c6c22f"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "b96623e367bd8bc3", "uuid": "8ab8869f-0b1d-43de-872c-9bf4f3adaeb1"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "c6b3e47f9c11596c", "uuid": "f40112b7-48c5-4f23-9f21-63d8e091f6d0"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "7a0f2dde2b5d6619", "uuid": "2dba0c16-785b-4d60-b078-f08b165dbe1d"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "067ce3c7e559f632", "uuid": "19c6616d-8ef1-40b5-970c-d854e8fb9dbe"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "8363c828b832effc", "uuid": "7f70cb84-5b0e-48dc-aa87-e52282e370d6"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "23fa57f602461511", "uuid": "a20f6f57-2422-4dc6-a170-003a926b0a67"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "764ef33b86dc4158", "uuid": "e5f1280d-9dd8-48f4-bc74-cf5585849fc4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.rare(shared=input_otu.dat,bygroup=false,nseqs=1)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.unique.pick.dat\ninput_otu.0.01.pick.dat\ninput_otu.0.02.pick.dat\ninput_otu.0.03.pick.dat\ninput_otu.0.04.pick.dat\ninput_otu.0.05.pick.dat\ninput_otu.0.06.pick.dat\ninput_otu.0.07.pick.dat\ninput_otu.0.08.pick.dat\ninput_otu.0.09.pick.dat\ninput_otu.0.10.pick.dat\ninput_otu.0.11.pick.dat\ninput_otu.0.12.pick.dat\ninput_otu.0.13.pick.dat\ninput_otu.0.14.pick.dat\ninput_otu.0.15.pick.dat\ninput_otu.0.16.pick.dat\ninput_otu.0.17.pick.dat\ninput_otu.0.18.pick.dat\ninput_otu.0.19.pick.dat\ninput_otu.0.20.pick.dat\ninput_otu.0.21.pick.dat\ninput_otu.0.22.pick.dat\ninput_otu.0.23.pick.dat\ninput_otu.0.24.pick.dat\ninput_otu.0.25.pick.dat\ninput_otu.0.26.pick.dat\ninput_otu.0.27.pick.dat\ninput_otu.0.29.pick.dat\ninput_otu.0.32.pick.dat\ninput_otu.0.33.pick.dat\ninput_otu.0.36.pick.dat\ninput_otu.0.38.pick.dat\ninput_otu.0.41.pick.dat\ninput_otu.0.45.pick.dat\ninput_otu.0.55.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2457.dat' input_otu.dat &&  echo 'remove.rare( shared=input_otu.dat, bygroup=false, nseqs=1 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:19:05.076315", "params": {"input": "{\"__current_case__\": 0, \"label\": null, \"source\": \"shared\", \"groups\": null, \"bygroup\": \"false\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2457}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "nseqs": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "705", "id": "ce49eab21f44c35b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_rare.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input|bygroup": true, "input|source": "shared", "input|groups": ["forest", "pasture"], "input|label": ["0.05", "0.22", "0.41"], "input|otu": {"src": "hda", "id": "4eb6ee5cb7ab7d0b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "4eb6ee5cb7ab7d0b", "uuid": "558df565-4a9f-4e34-b432-7fd50da71a74"}}, "update_time": "2018-02-08T18:19:29.011991", "tool_id": "mothur_remove_rare", "outputs": {"__new_primary_file_0.41|0.05__": {"src": "hda", "id": "91b58ed15e4e89f3", "uuid": "7d23c7ed-f52c-43f9-a44e-5629055963a1"}, "logfile": {"src": "hda", "id": "7fb409cd94387402", "uuid": "63b2a24b-bc3a-4645-ac16-d548c4dc3540"}, "__new_primary_file_0.41|0.22__": {"src": "hda", "id": "40de2667ff1e222c", "uuid": "e99fecc8-1e4a-4744-bf80-74d4b84e13db"}, "__new_primary_file_0.41|0.41__": {"src": "hda", "id": "bed855b2598b1c7b", "uuid": "0876d651-f17d-43d0-8aa9-a02a1ea5f3af"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.rare(shared=input_otu.dat,bygroup=true,groups=forest-pasture,lab \rel=0.05-0.22-0.41,nseqs=1)\n0.05\n0.22\n0.41\n\nOutput File Names: \ninput_otu.0.05.pick.dat\ninput_otu.0.22.pick.dat\ninput_otu.0.41.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2495.dat' input_otu.dat &&  echo 'remove.rare( shared=input_otu.dat, bygroup=true, groups=forest-pasture, label=0.05-0.22-0.41, nseqs=1 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:19:25.682198", "params": {"input": "{\"__current_case__\": 0, \"label\": [\"0.05\", \"0.22\", \"0.41\"], \"source\": \"shared\", \"groups\": [\"forest\", \"pasture\"], \"bygroup\": \"true\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2495}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "nseqs": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "818", "id": "5e64ba0eb7841b04", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_rare.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"input|source": "default", "input|otu": {"src": "hda", "id": "9a17ce6ea75b5c66"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "9a17ce6ea75b5c66", "uuid": "0bb489e2-6155-45bb-9c55-abcd6005d8f4"}}, "update_time": "2018-02-08T18:19:46.539468", "tool_id": "mothur_remove_rare", "outputs": {"logfile": {"src": "hda", "id": "e8e1ca0a2741d94b", "uuid": "1a71a491-0df2-4abb-8718-ae0417e59030"}, "pick_otu": {"src": "hda", "id": "773fd339f6505ca6", "uuid": "816dc85c-14d5-497e-8788-851d0d454a0d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.rare(sabund=input_otu.dat,nseqs=1)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2500.dat' input_otu.dat &&  echo 'remove.rare( sabund=input_otu.dat, nseqs=1 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:19:43.384733", "params": {"input": "{\"source\": \"default\", \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 2500}]}, \"__current_case__\": 2, \"label\": null}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "nseqs": "\"1\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "906", "id": "e561f0821a7a597e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_rare.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"accnos": {"src": "hda", "id": "071087e21ad6aa1c"}, "fasta_in": {"src": "hda", "id": "2543f1cad8cfe6a0"}, "dups": true}, "job": {"inputs": {"accnos": {"src": "hda", "id": "071087e21ad6aa1c", "uuid": "0a303147-c516-47a4-87d1-76275b3a1d87"}, "fasta_in": {"src": "hda", "id": "2543f1cad8cfe6a0", "uuid": "a84dc52b-f9a0-4db3-af0c-2a37f314d0a0"}}, "update_time": "2018-02-08T18:20:07.186595", "tool_id": "mothur_remove_seqs", "outputs": {"logfile": {"src": "hda", "id": "09b448289a70fe55", "uuid": "bd0555db-8faa-46df-9ed1-ffe62e57a2c6"}, "fasta_out": {"src": "hda", "id": "8534402e7f1fc070", "uuid": "d7e93696-6805-44b3-905f-0a4646138234"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.seqs(accnos=accnos.dat,fasta=fasta_in.dat)\nRemoved 3 sequences from your fasta file.\n\nOutput File Names: \nfasta_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2503.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2504.dat' fasta_in.dat && ln -s 'None' fastq_in.dat && ln -s 'None' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat &&  echo 'remove.seqs( accnos=accnos.dat ,fasta=fasta_in.dat  )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:20:04.111975", "params": {"fastq_in": "null", "dups": "\"true\"", "count_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1022", "id": "06788ac74a6156ce", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fastq_in": {"src": "hda", "id": "803a22dd93d75310"}, "accnos": {"src": "hda", "id": "7fcab135a6b69469"}}, "job": {"inputs": {"fastq_in": {"src": "hda", "id": "803a22dd93d75310", "uuid": "dbe6ac03-bfc0-4610-b76e-082ccfe2edb2"}, "accnos": {"src": "hda", "id": "7fcab135a6b69469", "uuid": "2666d05d-a61a-4485-a3ac-4fc14afbe333"}}, "update_time": "2018-02-08T18:20:22.881902", "tool_id": "mothur_remove_seqs", "outputs": {"logfile": {"src": "hda", "id": "9e8f20a034dacfe8", "uuid": "b7cb20a4-e2a9-43dd-b725-81d45c93b21d"}, "fastq_out": {"src": "hda", "id": "70e57fb8c96afc80", "uuid": "720c99b1-f772-434f-99fe-ac46d2f9c524"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.seqs(accnos=accnos.dat,fastq=fastq_in.dat)\nRemoved 3 sequences from your fastq file.\n\nOutput File Names: \nfastq_in.pick.dat\n\n[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2507.dat' accnos.dat && ln -s 'None' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2508.dat' fastq_in.dat && ln -s 'None' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat &&  echo 'remove.seqs( accnos=accnos.dat ,fastq=fastq_in.dat  )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:20:19.812919", "params": {"dups": "\"true\"", "fasta_in": "null", "count_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1152", "id": "202ba766860ff920", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fastq_in": {"src": "hda", "id": "c6cb321db749c627"}, "accnos": {"src": "hda", "id": "414d94e35f77b812"}, "fasta_in": {"src": "hda", "id": "9277a644c0099152"}, "dups": true}, "job": {"inputs": {"fastq_in": {"src": "hda", "id": "c6cb321db749c627", "uuid": "b01b576b-5d5a-45c8-bd25-7f45aeca49ce"}, "fasta_in": {"src": "hda", "id": "9277a644c0099152", "uuid": "c7b740b4-e49b-4bfe-837e-bc7f23c821ce"}, "accnos": {"src": "hda", "id": "414d94e35f77b812", "uuid": "ab991a10-c2b0-4de4-95f7-85fc1c564ac2"}}, "update_time": "2018-02-08T18:20:42.483186", "tool_id": "mothur_remove_seqs", "outputs": {"fasta_out": {"src": "hda", "id": "c127cc24451df342", "uuid": "4ce1cdd4-5b9f-44fa-9c5e-4319b1e4447e"}, "logfile": {"src": "hda", "id": "0601f5ddca2878d9", "uuid": "ce56505f-8263-4a3d-91e5-59f0bfaf5823"}, "fastq_out": {"src": "hda", "id": "d14c18ee2831b4fc", "uuid": "40716292-1893-46d8-978c-cbb3c47f4138"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.seqs(accnos=accnos.dat,fasta=fasta_in.dat,fastq=fastq_in.dat)\nRemoved 3 sequences from your fasta file.\nRemoved 3 sequences from your fastq file.\n\nOutput File Names: \nfasta_in.pick.dat\nfastq_in.pick.dat\n\n[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n\nmothur > quit\n\n\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\nDetected 1 [WARNING] messages, please review.\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2511.dat' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2512.dat' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2513.dat' fastq_in.dat && ln -s 'None' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat &&  echo 'remove.seqs( accnos=accnos.dat ,fasta=fasta_in.dat ,fastq=fastq_in.dat  )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:20:38.627569", "params": {"dups": "\"true\"", "count_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1349", "id": "e9e479aeb9b0a25e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"accnos": {"src": "hda", "id": "99d15eac4014af78"}, "count_in": {"src": "hda", "id": "b52f2aa5944e8b7f"}}, "job": {"inputs": {"accnos": {"src": "hda", "id": "99d15eac4014af78", "uuid": "d794f030-ebfd-4785-a36d-69378c3012ba"}, "count_in": {"src": "hda", "id": "b52f2aa5944e8b7f", "uuid": "70c52661-c5f1-4ff3-a00d-c53810b2ea9e"}}, "update_time": "2018-02-08T18:21:01.217167", "tool_id": "mothur_remove_seqs", "outputs": {"logfile": {"src": "hda", "id": "8711290f7ce753d2", "uuid": "b9fe3c0f-3a24-483f-b49c-89942a95af63"}, "count_out": {"src": "hda", "id": "bd3c4aa291ca99da", "uuid": "c7d68414-b083-4bfb-944d-d3f34d581333"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > remove.seqs(accnos=accnos.dat,count=count_in.dat)\nRemoved 8 sequences from your count file.\n\nOutput File Names: \ncount_in.pick.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2517.dat' accnos.dat && ln -s 'None' fasta_in.dat && ln -s 'None' fastq_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2518.dat' count_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' alignreport_in.dat && ln -s 'None' list_in.dat && ln -s 'None' taxonomy_in.dat &&  echo 'remove.seqs( accnos=accnos.dat ,count=count_in.dat  )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:20:58.127372", "params": {"fastq_in": "null", "dups": "\"true\"", "fasta_in": "null", "dbkey": "\"hg17\"", "group_in": "null", "taxonomy_in": "null", "alignreport_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "list_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1467", "id": "3fcf4993e0bb2ff7", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_remove_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "5eb53f4a9442659b"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "5eb53f4a9442659b", "uuid": "e3ddb07c-8bbc-41b4-93c4-ddff71162442"}}, "update_time": "2018-02-08T18:21:13.686851", "tool_id": "mothur_reverse_seqs", "outputs": {"logfile": {"src": "hda", "id": "65b29d046b1f849c", "uuid": "678bc632-03d6-4bfe-89b5-24cc0d8b74a6"}, "out_fasta": {"src": "hda", "id": "0b9cedc8ae8a94c2", "uuid": "56cac2ed-4bd3-4529-9b9f-ab9634842cf5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > reverse.seqs(fasta=fasta.dat)\n\nOutput File Names: \nfasta.rc.dat\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2521.dat' fasta.dat &&  echo 'reverse.seqs( fasta=fasta.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:21:10.537342", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1561", "id": "be25131031e1ad95", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_reverse_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "32ef23706aa388fb"}, "maxambig": "0", "maxlength": "275"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "32ef23706aa388fb", "uuid": "67e84174-fade-41d6-9981-d71cd3961247"}}, "update_time": "2018-02-08T18:21:26.199184", "tool_id": "mothur_screen_seqs", "outputs": {"contigsreport_out": {"src": "hda", "id": "56599abe680f3751", "uuid": "60282443-d360-48bc-96f4-6027bb560515"}, "logfile": {"src": "hda", "id": "685f126dc635c97c", "uuid": "b6de5901-d7e0-47f8-a4af-fe9c8ec96549"}, "bad_accnos": {"src": "hda", "id": "66f064aa8763a5a7", "uuid": "65936755-bd92-4c42-ac7e-45bb284a00dd"}, "alignreport_out": {"src": "hda", "id": "c93f720e91f61f32", "uuid": "6c7dfd89-f8b2-4678-8433-59016e725bb0"}, "fasta_out": {"src": "hda", "id": "05a76bb0530e159c", "uuid": "508e7c6a-89d5-4e3a-955e-c8a4e7995ad2"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > screen.seqs(fasta=fasta.dat,minlength=10,maxlength=275,maxambig=0,proce \rssors=1)\n\nUsing 1 processors.\nProcessing sequence: 25\n\nOutput File Names: \nfasta.good.dat\nfasta.bad.accnos\n\n\nIt took 0 secs to screen 25 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2524.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' groups.dat && ln -s 'None' qfile.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && ln -s 'None' summary.dat &&  echo 'screen.seqs( fasta=fasta.dat ,minlength=10 ,maxlength=275 ,maxambig=0 ,processors='\"${GALAXY_SLOTS:-8}\"' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:21:22.835146", "params": {"count": "null", "criteria": "\"-1\"", "optimize": "null", "end": "\"-1\"", "taxonomy": "null", "contigsrep": "{\"__current_case__\": 1, \"usecontigs\": \"no\"}", "maxhomop": "\"-1\"", "dbkey": "\"hg17\"", "summary": "null", "alignrep": "{\"usealign\": \"no\", \"__current_case__\": 1}", "start": "\"-1\"", "maxambig": "\"0\"", "names": "null", "groups": "null", "minlength": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "qfile": "null", "maxlength": "\"275\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1650", "id": "b07688f4168e93bf", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_screen_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "f0fe15730b8db9c4"}, "fasta": {"src": "hda", "id": "42af088b2abee145"}, "maxambig": "0", "maxlength": "500"}, "job": {"inputs": {"count": {"src": "hda", "id": "f0fe15730b8db9c4", "uuid": "7662f8fc-415b-4f23-9951-6eaea441232d"}, "fasta": {"src": "hda", "id": "42af088b2abee145", "uuid": "deb69949-3962-464d-b253-b02a76ae90b4"}}, "update_time": "2018-02-08T18:21:52.517139", "tool_id": "mothur_screen_seqs", "outputs": {"bad_accnos": {"src": "hda", "id": "37b038abf8b718f0", "uuid": "1127a6ef-c175-43ce-9605-0c783d3765d3"}, "count_out": {"src": "hda", "id": "00363558c5729a44", "uuid": "e46f23c4-7a89-4b61-8967-98adf21d4e77"}, "alignreport_out": {"src": "hda", "id": "4c2735cf7f715dcf", "uuid": "827bf85e-98b9-42a9-86bc-eccf04eb720f"}, "contigsreport_out": {"src": "hda", "id": "ba8cf376bccbc9b2", "uuid": "e128ed5f-7c04-41e8-bd39-cdcaf5965189"}, "fasta_out": {"src": "hda", "id": "c5b03287369c63ab", "uuid": "046994b4-43d1-4a23-9ecb-85c6db0420bb"}, "logfile": {"src": "hda", "id": "652751201af8821c", "uuid": "f869d649-38ad-4f61-a247-f3f3dcf2ba24"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > screen.seqs(fasta=fasta.dat,minlength=10,maxlength=500,maxambig=0,count \r=count.dat,processors=1)\n\nUsing 1 processors.\nProcessing sequence: 98\n\nOutput File Names: \nfasta.good.dat\nfasta.bad.accnos\ncount.good.dat\n\n\nIt took 0 secs to screen 98 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2530.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' groups.dat && ln -s 'None' qfile.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2531.dat' count.dat && ln -s 'None' taxonomy.dat && ln -s 'None' summary.dat &&  echo 'screen.seqs( fasta=fasta.dat ,minlength=10 ,maxlength=500 ,maxambig=0 ,count=count.dat ,processors='\"${GALAXY_SLOTS:-8}\"' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:21:48.991211", "params": {"criteria": "\"-1\"", "optimize": "null", "end": "\"-1\"", "taxonomy": "null", "qfile": "null", "maxhomop": "\"-1\"", "dbkey": "\"hg17\"", "summary": "null", "alignrep": "{\"usealign\": \"no\", \"__current_case__\": 1}", "start": "\"-1\"", "maxambig": "\"0\"", "names": "null", "groups": "null", "minlength": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "contigsrep": "{\"__current_case__\": 1, \"usecontigs\": \"no\"}", "maxlength": "\"500\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1773", "id": "978914f1b3729f41", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_screen_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"contigsrep|mismatches": "18", "maxambig": "0", "contigsrep|usecontigs": "yes", "maxlength": "275", "fasta": {"src": "hda", "id": "114c38d4ffc72675"}, "contigsrep|contigsreport": {"src": "hda", "id": "b0a3d3266cc35e70"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "114c38d4ffc72675", "uuid": "997523f7-3cce-4812-b622-533a7a716ac1"}, "contigsreport": {"src": "hda", "id": "b0a3d3266cc35e70", "uuid": "e0c873e8-a140-432a-8092-89ac2f8e8028"}}, "update_time": "2018-02-08T18:22:24.263577", "tool_id": "mothur_screen_seqs", "outputs": {"contigsreport_out": {"src": "hda", "id": "5872d7bb294e738e", "uuid": "18b00001-2f90-4f54-9212-e728eb0e9a4b"}, "logfile": {"src": "hda", "id": "cf5adbe5b084422c", "uuid": "29bae6ca-b02b-41b8-bdc2-c0ecb10264d4"}, "bad_accnos": {"src": "hda", "id": "e561361d04e2dadf", "uuid": "3f576845-eeea-41aa-bc25-ab12359708e1"}, "alignreport_out": {"src": "hda", "id": "17a1b993567aec5b", "uuid": "5d18a664-e9d3-4ec3-9dc2-a332b94e914e"}, "fasta_out": {"src": "hda", "id": "e1b9ee8eba60a340", "uuid": "f416f012-b80d-4d91-a13d-2582f23c8991"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > screen.seqs(fasta=fasta.dat,minlength=10,maxlength=275,maxambig=0,conti \rgsreport=contigsreport.dat,minoverlap=-1,ostart=-1,oend=-1,mismatches=18,process \rors=1)\n\nUsing 1 processors.\nProcessing sequence: 25\n\nOutput File Names: \ncontigsreport.good.contigs.report\nfasta.good.dat\nfasta.bad.accnos\n\n\nIt took 0 secs to screen 25 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2538.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' groups.dat && ln -s 'None' qfile.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && ln -s 'None' summary.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2539.dat' contigsreport.dat &&  echo 'screen.seqs( fasta=fasta.dat ,minlength=10 ,maxlength=275 ,maxambig=0 ,contigsreport=contigsreport.dat ,minoverlap=-1 ,ostart=-1 ,oend=-1 ,mismatches=18 ,processors='\"${GALAXY_SLOTS:-8}\"' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:22:20.100609", "params": {"count": "null", "criteria": "\"-1\"", "optimize": "null", "end": "\"-1\"", "taxonomy": "null", "contigsrep": "{\"oend\": \"-1\", \"contigsreport\": {\"values\": [{\"src\": \"hda\", \"id\": 2539}]}, \"ostart\": \"-1\", \"mismatches\": \"18\", \"usecontigs\": \"yes\", \"minoverlap\": \"-1\", \"__current_case__\": 0}", "maxhomop": "\"-1\"", "dbkey": "\"hg17\"", "summary": "null", "alignrep": "{\"usealign\": \"no\", \"__current_case__\": 1}", "start": "\"-1\"", "maxambig": "\"0\"", "names": "null", "groups": "null", "minlength": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "qfile": "null", "maxlength": "\"275\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "1890", "id": "071599f87a4de604", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_screen_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"alignrep|minscore": "100", "maxambig": "0", "alignrep|usealign": "yes", "maxlength": "275", "alignrep|alignreport": {"src": "hda", "id": "284b37b92e77841f"}, "fasta": {"src": "hda", "id": "5d1c7a267ee4549c"}}, "job": {"inputs": {"alignreport": {"src": "hda", "id": "284b37b92e77841f", "uuid": "faa386f7-f6d9-4b4e-8eca-e58fa2a6b0e8"}, "fasta": {"src": "hda", "id": "5d1c7a267ee4549c", "uuid": "350eb235-3d69-4cd0-8777-b0c22175248e"}}, "update_time": "2018-02-08T18:22:58.316487", "tool_id": "mothur_screen_seqs", "outputs": {"contigsreport_out": {"src": "hda", "id": "0f56156b04eb5a7c", "uuid": "33739706-afc6-45f6-939c-d47391d38deb"}, "logfile": {"src": "hda", "id": "8efa80d3971b8580", "uuid": "73a8ee94-8fd3-4da6-8134-ab8e859ade40"}, "bad_accnos": {"src": "hda", "id": "fe2332f09b9a6caf", "uuid": "e7738364-47d8-4f27-90f7-b964dcbafbcd"}, "alignreport_out": {"src": "hda", "id": "82c7032da1686dba", "uuid": "146b2158-8170-4ae8-894a-1100daa724f6"}, "fasta_out": {"src": "hda", "id": "e5f17aed15456c1d", "uuid": "8973d539-161c-48e0-947d-0825d21e6336"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > screen.seqs(fasta=fasta.dat,minlength=10,maxlength=275,maxambig=0,align \rreport=alignreport.dat,minsim=-1,minscore=100,maxinsert=-1,processors=1)\n\nUsing 1 processors.\nProcessing sequence: 22\n\nOutput File Names: \nalignreport.good.align.report\nfasta.good.dat\nfasta.bad.accnos\n\n\nIt took 0 secs to screen 22 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2545.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' groups.dat && ln -s 'None' qfile.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && ln -s 'None' summary.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2546.dat' alignreport.dat &&  echo 'screen.seqs( fasta=fasta.dat ,minlength=10 ,maxlength=275 ,maxambig=0 ,alignreport=alignreport.dat ,minsim=-1 ,minscore=100 ,maxinsert=-1 ,processors='\"${GALAXY_SLOTS:-8}\"' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:22:54.951671", "params": {"count": "null", "criteria": "\"-1\"", "optimize": "null", "end": "\"-1\"", "taxonomy": "null", "contigsrep": "{\"__current_case__\": 1, \"usecontigs\": \"no\"}", "maxhomop": "\"-1\"", "dbkey": "\"hg17\"", "summary": "null", "alignrep": "{\"usealign\": \"yes\", \"alignreport\": {\"values\": [{\"src\": \"hda\", \"id\": 2546}]}, \"__current_case__\": 0, \"minsim\": \"-1\", \"maxinsert\": \"-1\", \"minscore\": \"100\"}", "start": "\"-1\"", "maxambig": "\"0\"", "names": "null", "groups": "null", "minlength": "\"10\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "qfile": "null", "maxlength": "\"275\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2022", "id": "8cfece4559d4fc3b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_screen_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"matrix|method_name|count": {"src": "hda", "id": "ca5000435bda311d"}, "otu": {"src": "hda", "id": "bb539f073f00812b"}, "matrix|dist": {"src": "hda", "id": "220cf7d719dd1e3f"}}, "job": {"inputs": {"dist": {"src": "hda", "id": "ca5000435bda311d", "uuid": "e9a28efa-a393-44fa-967f-a0b7bd9ebf71"}, "otu": {"src": "hda", "id": "bb539f073f00812b", "uuid": "ba882201-0e75-49ee-9788-1e4c9eb91022"}, "matrix|count": {"src": "hda", "id": "ca5000435bda311d", "uuid": "e9a28efa-a393-44fa-967f-a0b7bd9ebf71"}}, "update_time": "2018-02-08T18:23:33.150499", "tool_id": "mothur_sens_spec", "outputs": {"sensspec": {"src": "hda", "id": "cd2710fe9c8e2a0a", "uuid": "f89fcbc4-fb42-49c8-a692-454e7f940363"}, "logfile": {"src": "hda", "id": "a6abaddda864dc74", "uuid": "a7d81a4b-2f77-4699-8769-23850fa276bb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sens.spec(list=otu.dat,column=matrix.dist.dat,count=matrix.method_name. \rcount.dat,precision=100,cutoff=-1.0)\n\nNOTE: sens.spec assumes that only unique sequences were used to generate the distance matrix.\n\nIt took 0 to run sens.spec.\n\nOutput File Names: \notu.sensspec\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2554.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2552.dat' matrix.dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2553.dat' matrix.method_name.count.dat &&   echo 'sens.spec( list=otu.dat, column=matrix.dist.dat, count=matrix.method_name.count.dat, precision=100, cutoff=-1.0 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:23:29.979676", "params": {"cutoff": "\"-1.0\"", "matrix": "{\"method_name\": {\"count\": {\"values\": [{\"src\": \"hda\", \"id\": 2553}]}, \"method\": \"count\", \"__current_case__\": 0}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 2552}]}, \"__current_case__\": 0, \"format\": \"column\"}", "precision": "\"100\"", "dbkey": "\"hg17\"", "label": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2173", "id": "29caadb190f2e006", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sens_spec.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"matrix|method_name|count": {"src": "hda", "id": "0b8bf891c9e392c5"}, "cutoff": "0.10", "otu": {"src": "hda", "id": "a770ee5c0aa4752d"}, "matrix|dist": {"src": "hda", "id": "276a286d69827381"}, "label": ["0.03", "0.05", "0.22"]}, "job": {"inputs": {"dist": {"src": "hda", "id": "0b8bf891c9e392c5", "uuid": "8c1fb6ef-8fb2-4f3b-9e5a-71f302eadb4e"}, "otu": {"src": "hda", "id": "a770ee5c0aa4752d", "uuid": "862748b0-5a4c-4a8e-9ce1-d484f0cea78f"}, "matrix|count": {"src": "hda", "id": "0b8bf891c9e392c5", "uuid": "8c1fb6ef-8fb2-4f3b-9e5a-71f302eadb4e"}}, "update_time": "2018-02-08T18:23:58.017498", "tool_id": "mothur_sens_spec", "outputs": {"sensspec": {"src": "hda", "id": "13e8a4ab78efa0c3", "uuid": "830b10f1-e3e1-4daf-9543-3a3c84272526"}, "logfile": {"src": "hda", "id": "0e1aeed8734b5624", "uuid": "f309d90b-da0b-488c-8acd-d7c88e5cfcf6"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sens.spec(list=otu.dat,column=matrix.dist.dat,count=matrix.method_name. \rcount.dat,label=0.03-0.05-0.22,label=0.03-0.05-0.22,precision=100,cutoff=0.1)\n\nNOTE: sens.spec assumes that only unique sequences were used to generate the distance matrix.\n\nIt took 0 to run sens.spec.\n\nOutput File Names: \notu.sensspec\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2559.dat' otu.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2557.dat' matrix.dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2558.dat' matrix.method_name.count.dat &&   echo 'sens.spec( list=otu.dat, column=matrix.dist.dat, count=matrix.method_name.count.dat, label=0.03-0.05-0.22, label=0.03-0.05-0.22, precision=100, cutoff=0.1 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:23:54.921822", "params": {"cutoff": "\"0.1\"", "matrix": "{\"method_name\": {\"count\": {\"values\": [{\"src\": \"hda\", \"id\": 2558}]}, \"method\": \"count\", \"__current_case__\": 0}, \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 2557}]}, \"__current_case__\": 0, \"format\": \"column\"}", "precision": "\"100\"", "dbkey": "\"hg17\"", "label": "[\"0.03\", \"0.05\", \"0.22\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2317", "id": "41cb101ab8c7143d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sens_spec.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment|template": {"src": "hda", "id": "3d56df3f9910bb65"}, "alignment|source": "history", "fasta_in": {"src": "hda", "id": "5244dd9a7b7ad1ff"}}, "job": {"inputs": {"fasta_in": {"src": "hda", "id": "5244dd9a7b7ad1ff", "uuid": "3cc67e25-f341-4480-b12f-daccd035f7c0"}, "template": {"src": "hda", "id": "3d56df3f9910bb65", "uuid": "0b126cee-0e8c-4f41-a425-0693293ee426"}}, "update_time": "2018-02-08T18:24:19.878364", "tool_id": "mothur_seq_error", "outputs": {"seq_reverse_out": {"src": "hda", "id": "8b42193f5326fbe1", "uuid": "4e9fe539-3b01-47d8-a593-57f6c554dbd9"}, "seq_forward_out": {"src": "hda", "id": "e18f72b039a3216a", "uuid": "e8c55d65-3633-425b-bbb2-5212ba243e6f"}, "count_out": {"src": "hda", "id": "42d2637b0f6e48e5", "uuid": "feb6bfc7-287a-432e-983b-a699b04999e1"}, "ref_query_out": {"src": "hda", "id": "f4fa5631199a49ea", "uuid": "231a8554-5816-4549-b52c-f67243a6f128"}, "matrix_out": {"src": "hda", "id": "244af713c6fa3d39", "uuid": "74ae8954-8372-4c96-8bd7-b2cdf5ea50da"}, "seq_out": {"src": "hda", "id": "a1cf0baa8d621c92", "uuid": "453d4d7f-fcd1-414d-94b7-dddcefe48909"}, "summary_out": {"src": "hda", "id": "26853ddf806efff5", "uuid": "fbca03a6-37ed-4926-a21a-e907093a45c7"}, "chimera_out": {"src": "hda", "id": "aefbd28d5fee1c64", "uuid": "7197202a-ba63-4414-94d7-83b30b16ff49"}, "logfile": {"src": "hda", "id": "ba0aff7639a35591", "uuid": "3aa03c30-d34e-4efb-9945-d30e19ca5f2f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > seq.error(fasta=fasta_in.dat,reference=alignment.template.dat,ignorechi \rmeras=true,aligned=T,processors=1)\n\nUsing 1 processors.\nIt took 0 to read 32 sequences.\n3\n\nMultiply error rate by 100 to obtain the percent sequencing errors.\nOverall error rate:\t-nan\nErrors\tSequences\n0\t0\n1\t0\n2\t0\n3\t0\n4\t0\n5\t0\n6\t0\n7\t0\n8\t0\n9\t0\n10\t0\nIt took 0 secs to check 3 sequences.\n\nOutput File Names: \nfasta_in.error.summary\nfasta_in.error.seq\nfasta_in.error.chimera\nfasta_in.error.seq.forward\nfasta_in.error.seq.reverse\nfasta_in.error.count\nfasta_in.error.matrix\nfasta_in.error.ref\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2562.dat' fasta_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2563.dat' alignment.template.dat &&  echo 'seq.error( fasta=fasta_in.dat, reference=alignment.template.dat, ignorechimeras=true, aligned=T, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:24:15.531119", "params": {"count": "null", "ignorechimeras": "\"true\"", "dbkey": "\"hg17\"", "qual": "{\"use\": \"no\", \"__current_case__\": 1}", "alignment": "{\"source\": \"history\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 2563}]}, \"__current_case__\": 1}", "threshold": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2427", "id": "e0b8f8f721986493", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_seq_error.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"alignment|source": "history", "fasta_in": {"src": "hda", "id": "1b8205f65139cc31"}, "alignment|template": {"src": "hda", "id": "c7d1feb17824923b"}, "qual|use": "yes", "qual|alignreport_in": {"src": "hda", "id": "d8dc82f61882a266"}, "qual|qfile_in": {"src": "hda", "id": "70da4f87b75aff13"}}, "job": {"inputs": {"fasta_in": {"src": "hda", "id": "1b8205f65139cc31", "uuid": "478ca9d3-322b-4068-b94f-0111b59efb11"}, "qfile_in": {"src": "hda", "id": "70da4f87b75aff13", "uuid": "19cdfb37-ff45-4d94-b11f-71656e9bd677"}, "template": {"src": "hda", "id": "c7d1feb17824923b", "uuid": "8b385164-a043-4860-957f-0c59305bea7d"}, "alignreport_in": {"src": "hda", "id": "d8dc82f61882a266", "uuid": "4248447c-9976-4a7d-9406-4ae5c33c2f2a"}}, "update_time": "2018-02-08T18:24:48.000084", "tool_id": "mothur_seq_error", "outputs": {"seq_reverse_out": {"src": "hda", "id": "3912249166cad271", "uuid": "bfc03af8-1d7c-40bb-97bc-982771be91dd"}, "seq_forward_out": {"src": "hda", "id": "f65e64aaf8a7f10a", "uuid": "2d8976df-abbb-41d7-963b-2cb994e4c835"}, "count_out": {"src": "hda", "id": "be576b0744534969", "uuid": "8826c8d6-32bc-4f2b-9ee6-7726fd2b62c0"}, "ref_query_out": {"src": "hda", "id": "903a94902fe885ed", "uuid": "cb6b9beb-3cd2-42ba-a8b8-ff547586997a"}, "matrix_out": {"src": "hda", "id": "0627c045bdb77024", "uuid": "48e3d2f5-2a04-451e-b40e-a3bed16a281a"}, "seq_out": {"src": "hda", "id": "04dcc2b07f73afca", "uuid": "96970c38-c54c-40e2-8ea7-a6af943ede96"}, "qual_forward_out": {"src": "hda", "id": "9a8ce407cbfa5454", "uuid": "b00274e3-fe1f-4fa9-bb5f-5a113e6d9f0a"}, "qual_reverse_out": {"src": "hda", "id": "73cb3a10e2a8b26b", "uuid": "26cba71c-8da2-4e9c-9584-d55a4b7809f4"}, "quality_out": {"src": "hda", "id": "d1fd239c001b68d8", "uuid": "a06f233b-442f-48a8-99f6-ae776f11dd42"}, "summary_out": {"src": "hda", "id": "87efef17dc7885df", "uuid": "8430a187-be22-468b-87ef-40a39cdcf0b1"}, "chimera_out": {"src": "hda", "id": "48b20c4302f2bed8", "uuid": "0515294f-48ed-461b-a2bc-a9a62c7a63c1"}, "logfile": {"src": "hda", "id": "876ad4f8f38f071f", "uuid": "6f101a55-e289-4b9f-a7f1-fda7481c8de4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > seq.error(fasta=fasta_in.dat,reference=alignment.template.dat,qfile=qfi \rle_in.dat,report=alignreport_in.dat,ignorechimeras=true,aligned=T,processors=1)\n\nUsing 1 processors.\nIt took 0 to read 32 sequences.\n10\n\nMultiply error rate by 100 to obtain the percent sequencing errors.\nOverall error rate:\t0.000790514\nErrors\tSequences\n0\t8\n1\t2\nIt took 0 secs to check 10 sequences.\n\nOutput File Names: \nfasta_in.error.summary\nfasta_in.error.seq\nfasta_in.error.chimera\nfasta_in.error.quality\nfasta_in.error.qual.forward\nfasta_in.error.qual.reverse\nfasta_in.error.seq.forward\nfasta_in.error.seq.reverse\nfasta_in.error.count\nfasta_in.error.matrix\nfasta_in.error.ref\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2573.dat' fasta_in.dat && ln -s 'None' name_in.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2574.dat' alignment.template.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2575.dat' qfile_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2576.dat' alignreport_in.dat &&  echo 'seq.error( fasta=fasta_in.dat, reference=alignment.template.dat, qfile=qfile_in.dat, report=alignreport_in.dat, ignorechimeras=true, aligned=T, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:24:42.401874", "params": {"count": "null", "ignorechimeras": "\"true\"", "dbkey": "\"hg17\"", "qual": "{\"use\": \"yes\", \"qfile_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2575}]}, \"__current_case__\": 0, \"alignreport_in\": {\"values\": [{\"src\": \"hda\", \"id\": 2576}]}}", "alignment": "{\"source\": \"history\", \"template\": {\"values\": [{\"src\": \"hda\", \"id\": 2574}]}, \"__current_case__\": 1}", "threshold": "\"\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2599", "id": "a4a6e47454aeba8e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_seq_error.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"sff": {"src": "hda", "id": "47a2e2cdac6d4f80"}, "sfftxt": true}, "job": {"inputs": {"sff": {"src": "hda", "id": "47a2e2cdac6d4f80", "uuid": "393c86c5-5fd7-4df8-a7e6-9f9789495e64"}}, "update_time": "2018-02-08T18:25:02.507559", "tool_id": "mothur_sffinfo", "outputs": {"out_sfftxt": {"src": "hda", "id": "f9c99ed753d12938", "uuid": "68756bfd-384a-4a42-a0c3-9859a7304837"}, "logfile": {"src": "hda", "id": "fd0620ae7484e07b", "uuid": "a5960cd3-cbb6-42ab-9c71-c454b280004e"}, "out_flow": {"src": "hda", "id": "c13713d4e8eb4016", "uuid": "2fb32b74-a179-4597-a87e-53ea9941bf22"}, "out_qfile": {"src": "hda", "id": "503dd82632d4ca26", "uuid": "50ee6fa5-42b8-47e5-ba7a-24dbd3831d13"}, "out_fasta": {"src": "hda", "id": "26a0fe97059939a7", "uuid": "211f0070-6853-4960-bfb8-c26a1873def5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sffinfo(sff=sff.dat,fasta=true,qfile=true,sfftxt=true,flow=true,trim=tr \rue)\nExtracting info from sff.dat ...\n10\nIt took 0 secs to extract 10.\n\nOutput File Names: \nsff.sff.txt\nsff.fasta\nsff.qual\nsff.flow\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2589.dat' sff.dat && ln -s 'None' accnos.dat &&  echo 'sffinfo( sff=sff.dat, fasta=true, qfile=true, sfftxt=true, flow=true, trim=true )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:24:58.805899", "params": {"trim": "\"true\"", "oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "qfile": "\"true\"", "flow": "\"true\"", "dbkey": "\"hg17\"", "sfftxt": "\"true\"", "fasta": "\"true\"", "accnos": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2700", "id": "e1d20895c4a97cda", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sffinfo.test_tool_000000", "has_data": true}, {"data": {"status": "failure", "inputs": {"sff": {"src": "hda", "id": "bb0ef3014c567e06"}, "oligo|add": "yes", "oligo|oligos": {"src": "hda", "id": "738c1dc0cd2bff09"}}, "output_problems": ["History item  different than expected\nOutput checksum [cfb0d0595dde77d45b4127bd3517bb78] does not match expected [f03c422fe364815e7214ad31ad135aca] (using hash algorithm md5)."], "job": {"inputs": {"sff": {"src": "hda", "id": "bb0ef3014c567e06", "uuid": "8d6a579c-7351-47ed-946f-102d71d327a5"}, "oligos": {"src": "hda", "id": "738c1dc0cd2bff09", "uuid": "11525dfc-de8b-495e-be2c-cb171928aa12"}}, "update_time": "2018-02-08T18:25:42.054096", "tool_id": "mothur_sffinfo", "outputs": {"logfile": {"src": "hda", "id": "3623f8401cdd50f2", "uuid": "e895e777-80e3-4570-acac-dc3653a75acf"}, "out_flow": {"src": "hda", "id": "2c561ba9c8e1003b", "uuid": "0d5af101-9f8c-431d-881a-5e3b1f0204c8"}, "out_qfile": {"src": "hda", "id": "1e46021b14d0447d", "uuid": "fad20474-627d-4fd3-bf9c-ea781849e5bc"}, "out_scrap": {"src": "hda", "id": "a3acd9d044b84d2e", "uuid": "13c1edf7-7864-452b-bebf-f91ff2a280f0"}, "out_fasta": {"src": "hda", "id": "9f2c5693ba5a738c", "uuid": "91304043-a44f-4fd7-be45-5a6c526ba7c1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sffinfo(sff=sff.dat,fasta=true,qfile=true,flow=true,trim=true,oligos=ol \rigo.oligos.dat,bdiffs=0,pdiffs=0,tdiffs=0,ldiffs=0,sdiffs=0)\nExtracting info from sff.dat ...\n10\nIt took 0 secs to extract 10.\n\nOutput File Names: \nsff.fasta\nsff.qual\nsff.flow\nsff.scrap.sff\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2595.dat' sff.dat && ln -s 'None' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2596.dat' oligo.oligos.dat &&  echo 'sffinfo( sff=sff.dat, fasta=true, qfile=true,  flow=true, trim=true ,oligos=oligo.oligos.dat ,bdiffs=0 ,pdiffs=0 ,tdiffs=0 ,ldiffs=0 ,sdiffs=0 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:25:38.219069", "params": {"trim": "\"true\"", "oligo": "{\"bdiffs\": \"0\", \"sdiffs\": \"0\", \"ldiffs\": \"0\", \"pdiffs\": \"0\", \"tdiffs\": \"0\", \"add\": \"yes\", \"__current_case__\": 1, \"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 2596}]}}", "qfile": "\"true\"", "flow": "\"true\"", "dbkey": "\"hg17\"", "sfftxt": "\"false\"", "fasta": "\"true\"", "accnos": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2822", "id": "227f734e4aa4c9b2", "user_email": "test@bx.psu.edu"}, "problem_log": "Traceback (most recent call last):\n  File \"/usr/lib/python2.7/unittest/case.py\", line 329, in run\n    testMethod()\n  File \"/tmp/saskia/tmpKSDp0p/galaxy-dev/test/functional/test_toolbox.py\", line 317, in test_tool\n    self.do_it(td)\n  File \"/tmp/saskia/tmpKSDp0p/galaxy-dev/test/functional/test_toolbox.py\", line 83, in do_it\n    raise e\nJobOutputsError: History item  different than expected\nOutput checksum [cfb0d0595dde77d45b4127bd3517bb78] does not match expected [f03c422fe364815e7214ad31ad135aca] (using hash algorithm md5).\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_mothur_sffinfo.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"prob|lookup": {"src": "hda", "id": "77320b12e7ef91b5"}, "prob|source": "hist", "flow": {"src": "hda", "id": "60c9b24d33e5937f"}}, "job": {"inputs": {"flow": {"src": "hda", "id": "60c9b24d33e5937f", "uuid": "8d46123d-b3f3-457f-ad4d-024a7458fd04"}, "lookup": {"src": "hda", "id": "77320b12e7ef91b5", "uuid": "c1a56757-fa60-4089-b4db-9369e2c4a563"}}, "update_time": "2018-02-08T18:26:26.039346", "tool_id": "mothur_shhh_flows", "outputs": {"shhh_qual": {"src": "hda", "id": "8e6e70ad3cbf6f5b", "uuid": "69442f06-4b7a-4d79-9770-a016c935e627"}, "shhh_fasta": {"src": "hda", "id": "d72069b333912103", "uuid": "bf6ce55b-137f-495e-b1c6-ee26b34f831b"}, "logfile": {"src": "hda", "id": "2a9e71b0254082e4", "uuid": "f11c3307-a478-43e9-9cb6-d86d89a9d4a0"}, "shhh_names": {"src": "hda", "id": "fdd8c264ffdf0e15", "uuid": "630abd25-463a-4776-8f78-158cdb5f1f01"}, "shhh_groups": {"src": "hda", "id": "146f0f4a4c131555", "uuid": "047263be-7f66-4515-85df-25d06897dbc5"}, "shhh_counts": {"src": "hda", "id": "818c72f58eb43f6e", "uuid": "2b64f07c-3445-420d-8470-adb7619c2d58"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > shhh.flows(flow=flow.dat,lookup=lookup.dat,maxiter=1000,mindelta=0.0000 \r01000000,cutoff=0.01,sigma=0.06,order=A,large=10000,processors=1)\n\nUsing 1 processors.\n\nDivided flow.dat into 1 files.\n\n\n>>>>>\tProcessing flow.dat0.temp (file 1 of 1)\t<<<<<\nReading flowgrams...\nIdentifying unique flowgrams...\nCalculating distances between flowgrams...\n0\t0\t3e-06\n92\t0\t0.007893\n\nTotal time: 0\t0.016342\n\nClustering flowgrams...\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\n\nDenoising 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08686\n983\t1.80003e-05\t-137.977\t0\t0.008962\n984\t1.7897e-05\t-137.977\t0\t0.008972\n985\t1.77943e-05\t-137.977\t0\t0.008752\n986\t1.76922e-05\t-137.977\t0\t0.008905\n987\t1.75907e-05\t-137.977\t0\t0.008841\n988\t1.74898e-05\t-137.977\t0\t0.008855\n989\t1.73895e-05\t-137.977\t0\t0.008889\n990\t1.72897e-05\t-137.977\t0\t0.008923\n991\t1.71905e-05\t-137.977\t0\t0.008746\n992\t1.70919e-05\t-137.977\t0\t0.008875\n993\t1.69938e-05\t-137.977\t0\t0.008746\n994\t1.68963e-05\t-137.977\t0\t0.008762\n995\t1.67994e-05\t-137.977\t0\t0.008854\n996\t1.6703e-05\t-137.977\t0\t0.008782\n997\t1.66071e-05\t-137.977\t0\t0.008768\n998\t1.65119e-05\t-137.977\t0\t0.0088\n999\t1.64171e-05\t-137.977\t0\t0.008842\n1000\t1.63229e-05\t-137.977\t0\t0.008814\n\nFinalizing...\nTotal time to process flow.dat:\t10\t9.25086\n\nOutput File Names: \nflow.shhh.qual\nflow.shhh.fasta\nflow.shhh.names\nflow.shhh.counts\nflow.shhh.groups\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2602.dat' flow.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2603.dat' lookup.dat &&  echo 'shhh.flows( flow=flow.dat, lookup=lookup.dat, maxiter=1000, mindelta=0.000001000000, cutoff=0.01, sigma=0.06, order=A, large=10000, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:26:13.200749", "params": {"cutoff": "\"0.01\"", "mindelta": "\"1e-06\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "order": "\"A\"", "large": "\"10000\"", "maxiter": "\"1000\"", "sigma": "\"0.06\"", "prob": "{\"source\": \"hist\", \"lookup\": {\"values\": [{\"src\": \"hda\", \"id\": 2603}]}, \"__current_case__\": 1}"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "2971", "id": "0a751ae1f530d3b0", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_shhh_flows.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "5777a6cd586901d1"}, "name": {"src": "hda", "id": "e133ff35d26a8aa1"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "5777a6cd586901d1", "uuid": "1cc6590e-9390-471b-a21c-74538fdc1b4a"}, "name": {"src": "hda", "id": "e133ff35d26a8aa1", "uuid": "cb099a08-1915-49f5-b316-653980bb6909"}}, "update_time": "2018-02-08T18:27:08.235372", "tool_id": "mothur_shhh_seqs", "outputs": {"shhh_fasta": {"src": "hda", "id": "b19ebbe1c1d1e884", "uuid": "d9994bf8-4f31-4d47-96fc-2f72512afb63"}, "logfile": {"src": "hda", "id": "a49605dd668f2992", "uuid": "9cc76af6-07f5-458a-878f-d84c573e7999"}, "shhh_map": {"src": "hda", "id": "e64b5914d8ba7854", "uuid": "5f9bd29b-c4a9-411d-8543-68f262cdc3b8"}, "shhh_names": {"src": "hda", "id": "3e4ace9eb2eabedd", "uuid": "5834d8cb-f75c-4513-9458-3678121edd82"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > shhh.seqs(fasta=fasta.dat,name=name.dat,sigma=0.01,processors=1)\n\nUsing 1 processors.\n\nCalculating distances...\n0\t0\n9\t0\nDone.\n/******************************************/\nRunning command: cluster(phylip=fasta.shhh.dist, method=furthest, cutoff=0.08)\n\nUsing 1 processors.\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\nunique\t2\t8\t1\n0.05\t2\t6\t2\nIt took 0 seconds to cluster\n\nOutput File Names: \nfasta.shhh.fn.sabund\nfasta.shhh.fn.rabund\nfasta.shhh.fn.list\n\n/******************************************/\n\nOutput File Names: \nfasta.shhh_seqs.map\nfasta.shhh_seqs.fasta\nfasta.shhh_seqs.names\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2610.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2611.dat' name.dat && ln -s 'None' group.dat &&  echo 'shhh.seqs( fasta=fasta.dat, name=name.dat, sigma=0.01, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:27:04.735094", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "group": "null", "sigma": "\"0.01\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3138", "id": "5bc2b2daf3f5f2ab", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_shhh_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta_in": {"src": "hda", "id": "1cd50e97ce5776f1"}}, "job": {"inputs": {"fasta_in": {"src": "hda", "id": "1cd50e97ce5776f1", "uuid": "9e7a7665-6ca5-4527-a9e9-a63baa6cbfed"}}, "update_time": "2018-02-08T18:27:39.681966", "tool_id": "mothur_sort_seqs", "outputs": {"logfile": {"src": "hda", "id": "346c6a409ca2df72", "uuid": "42f2fa77-d96e-4a9c-8939-d912cb67fc1a"}, "fasta_out": {"src": "hda", "id": "4628ae23f7bf7c59", "uuid": "8900356a-102f-4939-a96f-2d0a8afcf3b9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sort.seqs(fasta=fasta_in.dat,large=false)\n\nUsing fasta_in.dat to determine the order. It contains 98 sequences.\n\nOutput File Names: \nfasta_in.sorted.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2616.dat' fasta_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' flow_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' tax_in.dat && ln -s 'None' accnos.dat && ln -s 'None' count.dat &&  echo 'sort.seqs( fasta=fasta_in.dat, large=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:27:35.785519", "params": {"count": "null", "accnos": "null", "dbkey": "\"hg17\"", "large": "\"false\"", "group_in": "null", "tax_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "flow_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3256", "id": "25291f5c38a3933e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sort_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"qfile_in": {"src": "hda", "id": "824743428f8b7c8d"}}, "job": {"inputs": {"qfile_in": {"src": "hda", "id": "824743428f8b7c8d", "uuid": "c9c55f34-7a04-43e3-bb69-ac0f242ccad2"}}, "update_time": "2018-02-08T18:27:59.212444", "tool_id": "mothur_sort_seqs", "outputs": {"logfile": {"src": "hda", "id": "31e158d4a9000232", "uuid": "808de0d3-c1fc-4457-91df-b06e3bcfe3b4"}, "qfile_out": {"src": "hda", "id": "db53bbfda4df48de", "uuid": "cbf4ab99-8973-422b-bd93-f147f201103d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sort.seqs(qfile=qfile_in.dat,large=false)\n\nUsing qfile_in.dat to determine the order. It contains 25 sequences.\n\nOutput File Names: \nqfile_in.sorted.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s 'None' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2619.dat' qfile_in.dat && ln -s 'None' flow_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' tax_in.dat && ln -s 'None' accnos.dat && ln -s 'None' count.dat &&  echo 'sort.seqs( qfile=qfile_in.dat, large=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:27:56.051824", "params": {"count": "null", "fasta_in": "null", "dbkey": "\"hg17\"", "large": "\"false\"", "group_in": "null", "tax_in": "null", "accnos": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "flow_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3351", "id": "211e907a60c908e9", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sort_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"group_in": {"src": "hda", "id": "16d880b4edd0df2d"}}, "job": {"inputs": {"group_in": {"src": "hda", "id": "16d880b4edd0df2d", "uuid": "75b739f3-ddc0-4f71-9c88-3d21ab47d1e8"}}, "update_time": "2018-02-08T18:28:18.033002", "tool_id": "mothur_sort_seqs", "outputs": {"group_out": {"src": "hda", "id": "3f996a02633eb191", "uuid": "0dbf0bc4-fcc8-44d2-a46f-0a9215046bf8"}, "logfile": {"src": "hda", "id": "8cbd5613d4a60bc9", "uuid": "405d9f6c-ca17-411f-847c-25be73d2e6a7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sort.seqs(group=group_in.dat,large=false)\n\nUsing group_in.dat to determine the order. It contains 98 sequences.\n\nOutput File Names: \ngroup_in.sorted.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s 'None' fasta_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' flow_in.dat && ln -s 'None' name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2622.dat' group_in.dat && ln -s 'None' tax_in.dat && ln -s 'None' accnos.dat && ln -s 'None' count.dat &&  echo 'sort.seqs( group=group_in.dat, large=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:28:13.805640", "params": {"count": "null", "accnos": "null", "fasta_in": "null", "dbkey": "\"hg17\"", "large": "\"false\"", "tax_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "flow_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3445", "id": "0a2f8c1113cd2df5", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sort_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "8bf06e7b389a0ffb"}, "fasta_in": {"src": "hda", "id": "d1826c27f8cbf4a0"}}, "job": {"inputs": {"count": {"src": "hda", "id": "8bf06e7b389a0ffb", "uuid": "8e56c30e-7b59-4767-991f-d9688891c932"}, "fasta_in": {"src": "hda", "id": "d1826c27f8cbf4a0", "uuid": "98024751-92aa-4a52-aafd-26a9121a53e3"}}, "update_time": "2018-02-08T18:28:40.437807", "tool_id": "mothur_sort_seqs", "outputs": {"logfile": {"src": "hda", "id": "a300c5f999d0cfba", "uuid": "9ca6f143-214e-4fc6-adcc-6162c94689f3"}, "fasta_out": {"src": "hda", "id": "a46cf8d4ce36a708", "uuid": "16dd653a-47fd-4e16-bd9a-591390988f25"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sort.seqs(fasta=fasta_in.dat,count=count.dat,large=false)\n\nUsing fasta_in.dat to determine the order. It contains 98 sequences.\nOrdered 96 sequences from count.dat.\n\nOutput File Names: \nfasta_in.sorted.dat\ncount.sorted.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2625.dat' fasta_in.dat && ln -s 'None' qfile_in.dat && ln -s 'None' flow_in.dat && ln -s 'None' name_in.dat && ln -s 'None' group_in.dat && ln -s 'None' tax_in.dat && ln -s 'None' accnos.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2626.dat' count.dat &&  echo 'sort.seqs( fasta=fasta_in.dat, count=count.dat, large=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:28:37.404630", "params": {"accnos": "null", "dbkey": "\"hg17\"", "large": "\"false\"", "group_in": "null", "tax_in": "null", "qfile_in": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "flow_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3576", "id": "b2c5ddb42b4715c3", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sort_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"group_in": {"src": "hda", "id": "c76193b10ac0b663"}, "fasta_in": {"src": "hda", "id": "e706d88604ad5bf3"}, "qfile_in": {"src": "hda", "id": "ba12713cb9628bec"}}, "job": {"inputs": {"group_in": {"src": "hda", "id": "c76193b10ac0b663", "uuid": "c6a6d783-c7c1-493d-be2f-a876d6323589"}, "fasta_in": {"src": "hda", "id": "e706d88604ad5bf3", "uuid": "991a3a59-3d83-4fae-b11a-65f430fdd634"}, "qfile_in": {"src": "hda", "id": "ba12713cb9628bec", "uuid": "02124aba-f4fe-4838-ba90-cb365b9e2576"}}, "update_time": "2018-02-08T18:29:05.595883", "tool_id": "mothur_sort_seqs", "outputs": {"fasta_out": {"src": "hda", "id": "c7b310e48f70e08a", "uuid": "b17499bf-c0d5-4d5b-b7c3-9f4f404ec20b"}, "group_out": {"src": "hda", "id": "33554e7d04f7eca7", "uuid": "e3eafd81-6d26-49ba-9f8a-d6c6a9c8ad6e"}, "logfile": {"src": "hda", "id": "ebfc3f08b652b108", "uuid": "97d399d6-1351-47df-900d-f6ffaca100a0"}, "qfile_out": {"src": "hda", "id": "b04e7e1be4882fea", "uuid": "8ddadd71-545d-482b-a95b-0178f6f4931d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sort.seqs(fasta=fasta_in.dat,qfile=qfile_in.dat,group=group_in.dat,larg \re=false)\n\nUsing fasta_in.dat to determine the order. It contains 98 sequences.\nM00967_43_000000000-A3JHG_1_1101_19936_3208 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_15923_3823 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_14010_4122 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_10776_4204 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_22487_4260 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_13293_4703 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_24357_4866 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_23552_5194 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_7326_5417 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_11148_6457 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_7079_6722 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_8607_6805 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_15208_7185 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_4525_7317 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_9121_7358 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_8480_7498 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_11790_7581 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_20566_7622 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_10073_7632 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_5170_7771 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_18966_7778 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_5494_7973 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_10246_8076 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_23931_8157 was not in the contained the file which determined the order, adding it to the end.\nM00967_43_000000000-A3JHG_1_1101_18269_8162 was not in the contained the file which determined the order, adding it to the end.\nOrdered 25 sequences from qfile_in.dat.\nOrdered 98 sequences from group_in.dat.\n\nOutput File Names: \nfasta_in.sorted.dat\nqfile_in.sorted.dat\ngroup_in.sorted.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2629.dat' fasta_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2630.dat' qfile_in.dat && ln -s 'None' flow_in.dat && ln -s 'None' name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2631.dat' group_in.dat && ln -s 'None' tax_in.dat && ln -s 'None' accnos.dat && ln -s 'None' count.dat &&  echo 'sort.seqs( fasta=fasta_in.dat, qfile=qfile_in.dat, group=group_in.dat, large=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:29:02.185987", "params": {"count": "null", "dbkey": "\"hg17\"", "large": "\"false\"", "tax_in": "null", "accnos": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "flow_in": "null", "name_in": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3731", "id": "0b396aab4382c1fc", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sort_seqs.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"search|input": {"src": "hda", "id": "cdd1b52138ec3e26"}, "cutoff": "1", "fasta": {"src": "hda", "id": "9db5f5afb41f3f39"}, "search|type": "count", "accnos": true}, "job": {"inputs": {"input": {"src": "hda", "id": "cdd1b52138ec3e26", "uuid": "f97d3777-7d5a-496e-a5b7-7b011b6d852e"}, "fasta": {"src": "hda", "id": "9db5f5afb41f3f39", "uuid": "a7691f15-bd94-4b72-b433-456b92cec73b"}}, "update_time": "2018-02-08T18:29:36.918042", "tool_id": "mothur_split_abund", "outputs": {"rare_accnos": {"src": "hda", "id": "05138872ca68fd64", "uuid": "ea36fba9-61ad-42b7-b35f-5520c9a4d20b"}, "abund_accnos": {"src": "hda", "id": "a35b136816ca4ba6", "uuid": "3c3ae35d-b8cc-416d-9944-0e815e007ca2"}, "abund_count": {"src": "hda", "id": "91276d14d453a3b2", "uuid": "896492f3-c80a-4355-90ba-18c48015365b"}, "rare_count": {"src": "hda", "id": "63060f896ee9403e", "uuid": "2ec8cd6d-b418-41a4-a12f-016c3c9f4dec"}, "logfile": {"src": "hda", "id": "f678f751d18ba8c1", "uuid": "04e53333-620c-42af-bc0e-f31a264d2031"}, "rare_fasta": {"src": "hda", "id": "2efa83e2c9a3aa93", "uuid": "9c58ec60-46e1-467b-8277-c15fb5e74f9d"}, "abund_fasta": {"src": "hda", "id": "61dab379dc68ff95", "uuid": "dc7edc84-60bb-4e28-959e-2e9bbfb5cec4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > split.abund(fasta=fasta.dat,count=search_input.dat,accnos=true,cutoff=1 \r)\nYou cannot pick groups without group info in your count file; I will disregard your groups selection.\nU68620 is not in your names or list file, ignoring.\nU68667 is not in your names or list file, ignoring.\n\nOutput File Names: \nsearch_input.rare.count_table\nsearch_input.abund.count_table\nrare.accnos\nabund.accnos\nfasta.rare.fasta\nfasta.abund.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2636.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2637.dat' search_input.dat &&  echo 'split.abund( fasta=fasta.dat, count=search_input.dat, accnos=true, cutoff=1 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:29:33.061698", "params": {"cutoff": "\"1\"", "search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 2637}]}, \"type\": \"count\", \"__current_case__\": 2}", "dbkey": "\"hg17\"", "split": "{\"dosplit\": \"no\", \"__current_case__\": 1}", "accnos": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3854", "id": "35c110361200e678", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_split_abund.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"search|input": {"src": "hda", "id": "d7e1f95024c927b1"}, "cutoff": "1", "fasta": {"src": "hda", "id": "9cd1e40020f8e503"}, "search|type": "name", "accnos": true}, "job": {"inputs": {"input": {"src": "hda", "id": "d7e1f95024c927b1", "uuid": "7dc73945-9565-471d-b4fa-4bd8a597de34"}, "fasta": {"src": "hda", "id": "9cd1e40020f8e503", "uuid": "87d8b73f-3f9f-4a3a-afc6-813cec7c4224"}}, "update_time": "2018-02-08T18:30:27.641772", "tool_id": "mothur_split_abund", "outputs": {"abund_names": {"src": "hda", "id": "f791823f89c6163a", "uuid": "7aa7cb68-2cfc-4c17-9401-c1b551ecf743"}, "rare_names": {"src": "hda", "id": "d1ac60a58050f6ed", "uuid": "e4a6a0c5-eb4c-4d24-8617-1dc1aa54a082"}, "rare_accnos": {"src": "hda", "id": "db502a362bf63aa5", "uuid": "1e51b011-00bb-4ffa-8ccd-a0d66e5e5152"}, "abund_accnos": {"src": "hda", "id": "e3466765404e7b1c", "uuid": "247d27da-0689-4e33-b7d3-4b6235ba0cab"}, "logfile": {"src": "hda", "id": "fc26c44486a936db", "uuid": "19c47713-a360-477c-8985-ed31d2e2c3a4"}, "rare_fasta": {"src": "hda", "id": "ab82f8d568f8fb18", "uuid": "463dd8c9-26dd-4416-9b1a-6a5fd9f4c2df"}, "abund_fasta": {"src": "hda", "id": "11d9965bae4dbe18", "uuid": "efd16a42-3ca0-42c4-9844-963d7cfccc31"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > split.abund(fasta=fasta.dat,name=search_input.dat,accnos=true,cutoff=1) \r\u001b[A\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[K)\nU68620 is not in your names or list file, ignoring.\nU68667 is not in your names or list file, ignoring.\n\nOutput File Names: \nsearch_input.rare.names\nsearch_input.abund.names\nsearch_input.rare.accnos\nsearch_input.abund.accnos\nfasta.rare.fasta\nfasta.abund.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2645.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2646.dat' search_input.dat &&  echo 'split.abund( fasta=fasta.dat, name=search_input.dat, accnos=true, cutoff=1 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:30:23.593046", "params": {"cutoff": "\"1\"", "search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 2646}]}, \"type\": \"name\", \"__current_case__\": 0}", "dbkey": "\"hg17\"", "split": "{\"dosplit\": \"no\", \"__current_case__\": 1}", "accnos": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "3979", "id": "3f65e49d411bc75a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_split_abund.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"search|input": {"src": "hda", "id": "32fe67477db245f3"}, "cutoff": "1", "search|type": "name", "split|dosplit": "yes", "split|groups": ["forest", "pasture"], "split|group": {"src": "hda", "id": "3d0e97279f557300"}, "fasta": {"src": "hda", "id": "c2087ad656f5fd9b"}, "accnos": true}, "job": {"inputs": {"input": {"src": "hda", "id": "32fe67477db245f3", "uuid": "fdf6e7df-2c44-4074-9c6b-8bd1c696aac9"}, "fasta": {"src": "hda", "id": "c2087ad656f5fd9b", "uuid": "ebbabcec-254a-49dc-b629-f6187045222f"}, "group": {"src": "hda", "id": "3d0e97279f557300", "uuid": "9ea1d5dd-7a33-4e51-b05d-195c622a3e6d"}}, "update_time": "2018-02-08T18:31:24.163950", "tool_id": "mothur_split_abund", "outputs": {"abund_names": {"src": "hda", "id": "3220fd9000201448", "uuid": "1b92abd6-a9e4-443c-9ef2-4fbdce603b9f"}, "__new_primary_file_pasture|pasture__": {"src": "hda", "id": "b17c01ef6787726a", "uuid": "857bb644-caec-4d2e-a8cc-8c0a5a3a2ef2"}, "rare_accnos": {"src": "hda", "id": "8d1eae6dc7520e79", "uuid": "c3b60632-0579-497d-928e-f5220103ac0c"}, "abund_groups": {"src": "hda", "id": "61f64de29b08b609", "uuid": "bc78c0ea-7561-436d-9d35-d7e9f1f33acd"}, "rare_groups": {"src": "hda", "id": "cd67d5a3e6361697", "uuid": "a95f69ca-b6cc-474e-b34f-5502a685396a"}, "abund_accnos": {"src": "hda", "id": "52716b0ebe92fa96", "uuid": "5f2b1f65-bf25-44a4-8d30-07881af0d9ab"}, "__new_primary_file_pasture|forest__": {"src": "hda", "id": "546df6a89628ce23", "uuid": "06404d8a-b8cc-4666-b24b-14b417fa99e7"}, "logfile": {"src": "hda", "id": "0b9ed415b6d11582", "uuid": "b0cc327d-b3f1-4227-be98-ca2b7db2f6af"}, "rare_fasta": {"src": "hda", "id": "606329f9408a9a88", "uuid": "3653c7f2-b854-4803-9482-7f99fdaa5890"}, "abund_fasta": {"src": "hda", "id": "8cbfae124c6c8023", "uuid": "d9262219-3839-4331-8094-4823c755ccc1"}, "rare_names": {"src": "hda", "id": "ee2119e1cbbc112d", "uuid": "63d0f8b0-a860-4e54-8784-985282623795"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > split.abund(fasta=fasta.dat,name=search_input.dat,group=split_group.dat \r,groups=forest-pasture,accnos=true,cutoff=1)\nU68620 is not in your names or list file, ignoring.\nU68667 is not in your names or list file, ignoring.\n\nOutput File Names: \nsearch_input.forest.abund.names\nsearch_input.forest.rare.names\nsearch_input.pasture.abund.names\nsearch_input.pasture.rare.names\nsplit_group.forest.abund.groups\nsplit_group.forest.rare.groups\nsplit_group.pasture.abund.groups\nsplit_group.pasture.rare.groups\nsearch_input.forest.abund.accnos\nsearch_input.forest.rare.accnos\nsearch_input.pasture.abund.accnos\nsearch_input.pasture.rare.accnos\nfasta.forest.abund.fasta\nfasta.forest.rare.fasta\nfasta.pasture.abund.fasta\nfasta.pasture.rare.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2654.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2655.dat' search_input.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2656.dat' split_group.dat &&  echo 'split.abund( fasta=fasta.dat, name=search_input.dat, group=split_group.dat, groups=forest-pasture, accnos=true, cutoff=1 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:31:18.285897", "params": {"cutoff": "\"1\"", "search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 2655}]}, \"type\": \"name\", \"__current_case__\": 0}", "dbkey": "\"hg17\"", "split": "{\"dosplit\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 2656}]}, \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 0}", "accnos": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/727/galaxy_727.sh: line 40: [: /tmp/saskia/tmpKSDp0p/job_working_directory/000/727/working/fasta.forest.abund.fasta: binary operator expected\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/727/galaxy_727.sh: line 40: [: /tmp/saskia/tmpKSDp0p/job_working_directory/000/727/working/fasta.forest.rare.fasta: binary operator expected\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/727/galaxy_727.sh: line 40: [: /tmp/saskia/tmpKSDp0p/job_working_directory/000/727/working/search_input.forest.abund.names: binary operator expected\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/727/galaxy_727.sh: line 40: [: /tmp/saskia/tmpKSDp0p/job_working_directory/000/727/working/search_input.forest.rare.names: binary operator expected\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/727/galaxy_727.sh: line 40: [: /tmp/saskia/tmpKSDp0p/job_working_directory/000/727/working/search_input.forest.abund.accnos: binary operator expected\n/tmp/saskia/tmpKSDp0p/job_working_directory/000/727/galaxy_727.sh: line 40: [: /tmp/saskia/tmpKSDp0p/job_working_directory/000/727/working/search_input.forest.rare.accnos: binary operator expected\n", "job_metrics": [], "model_class": "Job", "external_id": "4120", "id": "8398b6d40e2a8a5d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_split_abund.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"search|input": {"src": "hda", "id": "a91c1fc0bea9aceb"}, "cutoff": "2", "search|type": "list", "split|dosplit": "yes", "split|groups": ["forest", "pasture"], "split|group": {"src": "hda", "id": "38625663880471ee"}, "fasta": {"src": "hda", "id": "9d6afbc2e4d51931"}, "accnos": true}, "job": {"inputs": {"input": {"src": "hda", "id": "a91c1fc0bea9aceb", "uuid": "e90e80a1-a39b-4caa-a737-1cc3a752ad15"}, "fasta": {"src": "hda", "id": "9d6afbc2e4d51931", "uuid": "077c9849-0f47-47e2-b871-4e78e1e080e4"}, "group": {"src": "hda", "id": "38625663880471ee", "uuid": "34f1049d-d4a0-4016-8bb1-9624460bac3f"}}, "update_time": "2018-02-08T18:33:04.548476", "tool_id": "mothur_split_abund", "outputs": 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"26c0054211fe320f", "uuid": "08e089c0-49df-42b7-8e4b-77a493ed56d9"}, "__new_primary_file_unique.pasture|0.32.forest__": {"src": "hda", "id": "0c5bf0fee2c9f2f2", "uuid": "54703ca7-1b6b-425e-99e3-9b443b9dc764"}, "__new_primary_file_unique.pasture|0.26.pasture__": {"src": "hda", "id": "ed3993a642a536c2", "uuid": "55fda38d-9035-46c3-9479-4ba397cd8e96"}, "__new_primary_file_pasture.unique|forest.0.25__": {"src": "hda", "id": "d4e6425fff4b7b44", "uuid": "dbaa8103-4e50-4ccc-a63d-d6f071d35ec8"}, "__new_primary_file_unique.pasture|0.15.pasture__": {"src": "hda", "id": "e07ab57151a51654", "uuid": "f0ea7182-bb30-4012-bf7e-06f2c98ecff8"}, "__new_primary_file_unique.pasture|0.36.pasture__": {"src": "hda", "id": "aaff7b2db40e0f9b", "uuid": "bde40b31-480e-43fc-b06c-90caf6fa0966"}, "__new_primary_file_unique.pasture|0.24.forest__": {"src": "hda", "id": "d7b4881ce8f2a650", "uuid": "403d4138-0734-4e0e-beb8-37b8fed1c9a5"}, "__new_primary_file_pasture.unique|forest.0.11__": {"src": "hda", "id": "0f9d27ef44328c88", "uuid": "4f8c9396-37ca-4d86-bbf6-3af3f9bd3514"}, "__new_primary_file_unique.pasture|0.14.pasture__": {"src": "hda", "id": "d7384c1e0a3adbb9", "uuid": "224cc942-84dc-4272-ae33-0ffd664c3469"}, "__new_primary_file_pasture.unique|forest.0.36__": {"src": "hda", "id": "786cdb8512e719d3", "uuid": "29a13eb1-237f-4fb9-8de7-2b92ba28252f"}, "__new_primary_file_pasture.unique|forest.0.17__": {"src": "hda", "id": "80bae1ac661749cb", "uuid": "8d07c84c-4f29-4ffb-ae7b-c98646daf9a6"}, "__new_primary_file_unique.pasture|0.41.pasture__": {"src": "hda", "id": "cdd00c2f56d70d8c", "uuid": "263e2a70-b626-454e-b16e-4d7bc06ff47d"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > split.abund(fasta=fasta.dat,list=search_input.dat,group=split_group.dat \r,groups=forest-pasture,accnos=true,cutoff=2)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \nsearch_input.forest.unique.rare.list\nsearch_input.forest.unique.abund.list\nsearch_input.pasture.unique.rare.list\nsearch_input.pasture.unique.abund.list\nsplit_group.unique.forest.abund.groups\nsplit_group.unique.forest.rare.groups\nsplit_group.unique.pasture.abund.groups\nsplit_group.unique.pasture.rare.groups\nsearch_input.unique.forest.abund.accnos\nsearch_input.unique.forest.rare.accnos\nsearch_input.unique.pasture.abund.accnos\nsearch_input.unique.pasture.rare.accnos\nfasta.unique.forest.abund.fasta\nfasta.unique.forest.rare.fasta\nfasta.unique.pasture.abund.fasta\nfasta.unique.pasture.rare.fasta\nsearch_input.forest.0.01.rare.list\nsearch_input.forest.0.01.abund.list\nsearch_input.pasture.0.01.rare.list\nsearch_input.pasture.0.01.abund.list\nsplit_group.0.01.forest.abund.groups\nsplit_group.0.01.forest.rare.groups\nsplit_group.0.01.pasture.abund.groups\nsplit_group.0.01.pasture.rare.groups\nsearch_input.0.01.forest.abund.accnos\nsearch_input.0.01.forest.rare.accnos\nsearch_input.0.01.pasture.abund.accnos\nsearch_input.0.01.pasture.rare.accnos\nfasta.0.01.forest.abund.fasta\nfasta.0.01.forest.rare.fasta\nfasta.0.01.pasture.abund.fasta\nfasta.0.01.pasture.rare.fasta\nsearch_input.forest.0.02.rare.list\nsearch_input.forest.0.02.abund.list\nsearch_input.pasture.0.02.rare.list\nsearch_input.pasture.0.02.abund.list\nsplit_group.0.02.forest.abund.groups\nsplit_group.0.02.forest.rare.groups\nsplit_group.0.02.pasture.abund.groups\nsplit_group.0.02.pasture.rare.groups\nsearch_input.0.02.forest.abund.accnos\nsearch_input.0.02.forest.rare.accnos\nsearch_input.0.02.pasture.abund.accnos\nsearch_input.0.02.pasture.rare.accnos\nfasta.0.02.forest.abund.fasta\nfasta.0.02.forest.rare.fasta\nfasta.0.02.pasture.abund.fasta\nfasta.0.02.pasture.rare.fasta\nsearch_input.forest.0.03.rare.list\nsearch_input.forest.0.03.abund.list\nsearch_input.pasture.0.03.rare.list\nsearch_input.pasture.0.03.abund.list\nsplit_group.0.03.forest.abund.groups\nsplit_group.0.03.forest.rare.groups\nsplit_group.0.03.pasture.abund.groups\nsplit_group.0.03.pasture.rare.groups\nsearch_input.0.03.forest.abund.accnos\nsearch_input.0.03.forest.rare.accnos\nsearch_input.0.03.pasture.abund.accnos\nsearch_input.0.03.pasture.rare.accnos\nfasta.0.03.forest.abund.fasta\nfasta.0.03.forest.rare.fasta\nfasta.0.03.pasture.abund.fasta\nfasta.0.03.pasture.rare.fasta\nsearch_input.forest.0.04.rare.list\nsearch_input.forest.0.04.abund.list\nsearch_input.pasture.0.04.rare.list\nsearch_input.pasture.0.04.abund.list\nsplit_group.0.04.forest.abund.groups\nsplit_group.0.04.forest.rare.groups\nsplit_group.0.04.pasture.abund.groups\nsplit_group.0.04.pasture.rare.groups\nsearch_input.0.04.forest.abund.accnos\nsearch_input.0.04.forest.rare.accnos\nsearch_input.0.04.pasture.abund.accnos\nsearch_input.0.04.pasture.rare.accnos\nfasta.0.04.forest.abund.fasta\nfasta.0.04.forest.rare.fasta\nfasta.0.04.pasture.abund.fasta\nfasta.0.04.pasture.rare.fasta\nsearch_input.forest.0.05.rare.list\nsearch_input.forest.0.05.abund.list\nsearch_input.pasture.0.05.rare.list\nsearch_input.pasture.0.05.abund.list\nsplit_group.0.05.forest.abund.groups\nsplit_group.0.05.forest.rare.groups\nsplit_group.0.05.pasture.abund.groups\nsplit_group.0.05.pasture.rare.groups\nsearch_input.0.05.forest.abund.accnos\nsearch_input.0.05.forest.rare.accnos\nsearch_input.0.05.pasture.abund.accnos\nsearch_input.0.05.pasture.rare.accnos\nfasta.0.05.forest.abund.fasta\nfasta.0.05.forest.rare.fasta\nfasta.0.05.pasture.abund.fasta\nfasta.0.05.pasture.rare.fasta\nsearch_input.forest.0.06.rare.list\nsearch_input.forest.0.06.abund.list\nsearch_input.pasture.0.06.rare.list\nsearch_input.pasture.0.06.abund.list\nsplit_group.0.06.forest.abund.groups\nsplit_group.0.06.forest.rare.groups\nsplit_group.0.06.pasture.abund.groups\nsplit_group.0.06.pasture.rare.groups\nsearch_input.0.06.forest.abund.accnos\nsearch_input.0.06.forest.rare.accnos\nsearch_input.0.06.pasture.abund.accnos\nsearch_input.0.06.pasture.rare.accnos\nfasta.0.06.forest.abund.fasta\nfasta.0.06.forest.rare.fasta\nfasta.0.06.pasture.abund.fasta\nfasta.0.06.pasture.rare.fasta\nsearch_input.forest.0.07.rare.list\nsearch_input.forest.0.07.abund.list\nsearch_input.pasture.0.07.rare.list\nsearch_input.pasture.0.07.abund.list\nsplit_group.0.07.forest.abund.groups\nsplit_group.0.07.forest.rare.groups\nsplit_group.0.07.pasture.abund.groups\nsplit_group.0.07.pasture.rare.groups\nsearch_input.0.07.forest.abund.accnos\nsearch_input.0.07.forest.rare.accnos\nsearch_input.0.07.pasture.abund.accnos\nsearch_input.0.07.pasture.rare.accnos\nfasta.0.07.forest.abund.fasta\nfasta.0.07.forest.rare.fasta\nfasta.0.07.pasture.abund.fasta\nfasta.0.07.pasture.rare.fasta\nsearch_input.forest.0.08.rare.list\nsearch_input.forest.0.08.abund.list\nsearch_input.pasture.0.08.rare.list\nsearch_input.pasture.0.08.abund.list\nsplit_group.0.08.forest.abund.groups\nsplit_group.0.08.forest.rare.groups\nsplit_group.0.08.pasture.abund.groups\nsplit_group.0.08.pasture.rare.groups\nsearch_input.0.08.forest.a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e.abund.groups\nsplit_group.0.45.pasture.rare.groups\nsearch_input.0.45.forest.abund.accnos\nsearch_input.0.45.forest.rare.accnos\nsearch_input.0.45.pasture.abund.accnos\nsearch_input.0.45.pasture.rare.accnos\nfasta.0.45.forest.abund.fasta\nfasta.0.45.forest.rare.fasta\nfasta.0.45.pasture.abund.fasta\nfasta.0.45.pasture.rare.fasta\nsearch_input.forest.0.55.rare.list\nsearch_input.forest.0.55.abund.list\nsearch_input.pasture.0.55.rare.list\nsearch_input.pasture.0.55.abund.list\nsplit_group.0.55.forest.abund.groups\nsplit_group.0.55.forest.rare.groups\nsplit_group.0.55.pasture.abund.groups\nsplit_group.0.55.pasture.rare.groups\nsearch_input.0.55.forest.abund.accnos\nsearch_input.0.55.forest.rare.accnos\nsearch_input.0.55.pasture.abund.accnos\nsearch_input.0.55.pasture.rare.accnos\nfasta.0.55.forest.abund.fasta\nfasta.0.55.forest.rare.fasta\nfasta.0.55.pasture.abund.fasta\nfasta.0.55.pasture.rare.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2682.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2683.dat' search_input.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/002/dataset_2684.dat' split_group.dat &&  echo 'split.abund( fasta=fasta.dat, list=search_input.dat, group=split_group.dat, groups=forest-pasture, accnos=true, cutoff=2 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:32:21.857882", "params": {"cutoff": "\"2\"", "search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 2683}]}, \"type\": \"list\", \"__current_case__\": 1, \"label\": null}", "dbkey": "\"hg17\"", "split": "{\"dosplit\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 2684}]}, \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 0}", "accnos": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "4268", "id": "a97fae24847b82ef", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_split_abund.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"search|input": {"src": "hda", "id": "38360e2d3ab06177"}, "cutoff": "2", "search|type": "list", "split|dosplit": "yes", "split|group": {"src": "hda", "id": "7fd9dcdabb947ccd"}, "split|groups": ["forest", "pasture"], "search|label": ["0.05", "0.22"], "fasta": {"src": "hda", "id": "5a062b1ff6cc9d5a"}, "accnos": true}, "job": {"inputs": {"input": {"src": "hda", "id": "38360e2d3ab06177", "uuid": "d0b2ed14-9037-4dd5-ae88-b7585e53d01d"}, "fasta": {"src": "hda", "id": "5a062b1ff6cc9d5a", "uuid": "a5a3ef3b-52e9-49cc-a4fc-8c86ccf0771e"}, "group": {"src": "hda", "id": "7fd9dcdabb947ccd", "uuid": "fd5545e9-1c74-45f8-afdb-aac61299fd9c"}}, "update_time": "2018-02-08T18:34:21.332942", "tool_id": "mothur_split_abund", "outputs": {"__new_primary_file_0.22.pasture|0.22.pasture__": {"src": "hda", "id": "d16be2ae47deec72", "uuid": "e0e1bc85-d362-4c10-99ed-37f4e5dc12a9"}, "__new_primary_file_pasture.0.22|forest.0.05__": {"src": "hda", "id": "ab54917a7131c881", "uuid": "6d56c002-39f5-47ab-8a9c-09b75b732005"}, "__new_primary_file_pasture.0.22|forest.0.22__": {"src": "hda", "id": "8e584b6d1dcf6293", "uuid": "377f5b7d-fdf7-477e-ba68-467ec6554408"}, "__new_primary_file_0.22.pasture|0.05.pasture__": {"src": "hda", "id": "b9aa8dda8024d3ce", "uuid": "daaa40c3-883f-47f0-95d1-33311618cfc4"}, "__new_primary_file_pasture.0.22|pasture.0.22__": {"src": "hda", "id": "28b0a5b79d875620", "uuid": "e01a2820-65d9-403c-9adf-6c096bd2a8eb"}, "__new_primary_file_0.22.pasture|0.05.forest__": {"src": "hda", "id": "44d57fb3b86c5aae", "uuid": "be5f6fb8-3477-45f8-b5cc-be9589ef8d22"}, "__new_primary_file_pasture.0.22|pasture.0.05__": {"src": "hda", "id": "bb320b551226491d", "uuid": "50a0d19c-a9cb-4bf5-9cc5-0347397aa46b"}, "logfile": {"src": "hda", "id": "90c7d1a0099e9a76", "uuid": "2419fe03-fbd8-4951-971c-a1e31e00592b"}, "__new_primary_file_0.22.pasture|0.22.forest__": {"src": "hda", "id": "51ecdd8f7307fd69", "uuid": "6819aa98-7c97-4468-a665-c3b4033568b5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > split.abund(fasta=fasta.dat,list=search_input.dat,label=0.05-0.22,group \r=split_group.dat,groups=forest-pasture,accnos=true,cutoff=2)\n0.05\n0.22\n\nOutput File Names: \nsearch_input.forest.0.05.rare.list\nsearch_input.forest.0.05.abund.list\nsearch_input.pasture.0.05.rare.list\nsearch_input.pasture.0.05.abund.list\nsplit_group.0.05.forest.abund.groups\nsplit_group.0.05.forest.rare.groups\nsplit_group.0.05.pasture.abund.groups\nsplit_group.0.05.pasture.rare.groups\nsearch_input.0.05.forest.abund.accnos\nsearch_input.0.05.forest.rare.accnos\nsearch_input.0.05.pasture.abund.accnos\nsearch_input.0.05.pasture.rare.accnos\nfasta.0.05.forest.abund.fasta\nfasta.0.05.forest.rare.fasta\nfasta.0.05.pasture.abund.fasta\nfasta.0.05.pasture.rare.fasta\nsearch_input.forest.0.22.rare.list\nsearch_input.forest.0.22.abund.list\nsearch_input.pasture.0.22.rare.list\nsearch_input.pasture.0.22.abund.list\nsplit_group.0.22.forest.abund.groups\nsplit_group.0.22.forest.rare.groups\nsplit_group.0.22.pasture.abund.groups\nsplit_group.0.22.pasture.rare.groups\nsearch_input.0.22.forest.abund.accnos\nsearch_input.0.22.forest.rare.accnos\nsearch_input.0.22.pasture.abund.accnos\nsearch_input.0.22.pasture.rare.accnos\nfasta.0.22.forest.abund.fasta\nfasta.0.22.forest.rare.fasta\nfasta.0.22.pasture.abund.fasta\nfasta.0.22.pasture.rare.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3262.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3263.dat' search_input.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3264.dat' split_group.dat &&  echo 'split.abund( fasta=fasta.dat, list=search_input.dat, label=0.05-0.22, group=split_group.dat, groups=forest-pasture, accnos=true, cutoff=2 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:34:15.959750", "params": {"cutoff": "\"2\"", "search": "{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 3263}]}, \"type\": \"list\", \"__current_case__\": 1, \"label\": [\"0.05\", \"0.22\"]}", "dbkey": "\"hg17\"", "split": "{\"dosplit\": \"yes\", \"group\": {\"values\": [{\"src\": \"hda\", \"id\": 3264}]}, \"groups\": [\"forest\", \"pasture\"], \"__current_case__\": 0}", "accnos": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "4425", "id": "9ecc9b17e1423ee8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_split_abund.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "94e36d9344f4dff1"}, "group": {"src": "hda", "id": "77055d672d3dfc70"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "94e36d9344f4dff1", "uuid": "bcb0a685-26a1-473e-8db2-731290c2d71a"}, "group": {"src": "hda", "id": "77055d672d3dfc70", "uuid": "2f686bf5-cc63-4dac-bacd-d82878b6663b"}}, "update_time": "2018-02-08T18:35:19.336599", "tool_id": "mothur_split_groups", "outputs": {"__new_primary_file_pasture|forest__": {"src": "hda", "id": "086a78d5d6cf5d6e", "uuid": "1f832a18-6aee-4670-a3a9-1d87ce78cfa1"}, "logfile": {"src": "hda", "id": "2ea441e22c11eebd", "uuid": "331204e8-c42f-4b25-b488-c5e55ea91543"}, "__new_primary_file_pasture|pasture__": {"src": "hda", "id": "ace7c95418a0de52", "uuid": "d11fd81b-73bd-4f17-9c52-a544e8145683"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > split.groups(fasta=fasta.dat,group=group.dat)\n\nProcessing group: forest\nProcessing group: pasture\n\nOutput File Names: \nfasta.forest.fasta\nfasta.pasture.fasta\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s 'None' name.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3298.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3299.dat' group.dat &&  echo 'split.groups( fasta=fasta.dat, group=group.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:35:16.412552", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "groups": "null", "name": "null"}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "4550", "id": "7ec799cf0545a3b8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_split_groups.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input|format": "list", "input|otu": {"src": "hda", "id": "2e7cb023461a16f4"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "2e7cb023461a16f4", "uuid": "838e9592-03b6-4a6c-836c-502754f9c3a1"}}, "update_time": "2018-02-08T18:35:43.597787", "tool_id": "mothur_sub_sample", "outputs": {"__new_primary_file_unique|0.10__": {"src": "hda", "id": "fd4a4a3fe46f280b", "uuid": "bc41ab14-c9f3-427b-a331-7c36da5d7dc7"}, "__new_primary_file_unique|0.05__": {"src": "hda", "id": "c64ee5ee7f79f0a6", "uuid": "cb5eb702-6ca0-43ff-add9-b7f2b7cf3450"}, "__new_primary_file_unique|0.17__": {"src": "hda", "id": "ec09a227354975ff", "uuid": "836f92e1-34ba-41e9-a565-3f77bde0324e"}, "__new_primary_file_unique|0.02__": {"src": "hda", "id": "45a337b5db97ab85", "uuid": "08901a22-bd50-4fb3-b244-041281afb8ff"}, "__new_primary_file_unique|0.21__": {"src": "hda", "id": "94fd33d364fcc131", "uuid": "107a3582-b007-4093-aa74-592e23bbd511"}, "__new_primary_file_unique|0.16__": {"src": "hda", "id": "c7c45b9b7153b04b", "uuid": "0c5d48a4-d3c2-4bbe-a53d-02a47be5b02e"}, "__new_primary_file_unique|0.45__": {"src": "hda", "id": "4c2ab93933e14931", "uuid": "91077f83-fe87-4f99-9827-17b0f990d620"}, "__new_primary_file_unique|0.03__": {"src": "hda", "id": "041847c37ff1f11d", "uuid": "15225a6a-10ef-4e9a-8a01-5bd335636c72"}, "__new_primary_file_unique|0.15__": {"src": "hda", "id": "fd10df936e5a6ffd", "uuid": "0595e1fb-4082-4417-af63-833df5b63f82"}, "__new_primary_file_unique|0.08__": {"src": "hda", "id": "db7b606431d708fd", "uuid": "7ad15d11-b0e7-41b9-99f3-b46a4628a7e8"}, "__new_primary_file_unique|0.14__": {"src": "hda", "id": "fedc92590bf7a1e3", "uuid": "036ed503-f693-4973-b57d-00786b4027ca"}, "__new_primary_file_unique|0.13__": {"src": "hda", "id": "fa68b0f5b7e3310f", "uuid": "1bb4262c-7f17-487d-b369-6fd216bdb468"}, "__new_primary_file_unique|0.09__": {"src": "hda", "id": "becaa11690574381", "uuid": "a5b3a3f3-3c59-44c0-b930-3e8db1d85e9d"}, "__new_primary_file_unique|0.12__": {"src": "hda", "id": "2b8bcf1bee106508", "uuid": "17439678-5ed0-4a85-a4d6-fa15666f7590"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "ca918f436c0404da", "uuid": "dd2c7108-a96c-4100-8d96-2785d0ffa2c7"}, "__new_primary_file_unique|0.11__": {"src": "hda", "id": "52ae354051a713cf", "uuid": "3ce96159-82e0-4e0e-a644-1522dd4ab280"}, "__new_primary_file_unique|0.41__": {"src": "hda", "id": "a21f6630d51aa237", "uuid": "6b2c9e56-d4b3-4deb-8f52-bee0305572cf"}, "__new_primary_file_unique|0.06__": {"src": "hda", "id": "e88c34232705ba65", "uuid": "81cafa7f-41d0-429e-8038-58cab8fc431b"}, "__new_primary_file_unique|0.25__": {"src": "hda", "id": "7c3a3946772cd3a5", "uuid": "9ac59227-fa48-4d82-85ad-75448bbced38"}, "__new_primary_file_unique|0.22__": {"src": "hda", "id": "25c2f28094be3e4a", "uuid": "a56e8353-e761-45df-820e-fb3342713ea7"}, "__new_primary_file_unique|0.36__": {"src": "hda", "id": "610851f8602f4f94", "uuid": "035d59ef-d1d7-4967-bb23-4fb16e3b5ed2"}, "__new_primary_file_unique|0.04__": {"src": "hda", "id": "3883bbf3e69f96c4", "uuid": "a42088ee-667c-44a9-b5ad-dd6b80141c6c"}, "__new_primary_file_unique|0.23__": {"src": "hda", "id": "c53c947799f8d062", "uuid": "0f9e30d9-8dbf-4829-8584-0bbdce6be1e1"}, "__new_primary_file_unique|0.33__": {"src": "hda", "id": "dccae4d18ce46393", "uuid": "1e44f7be-25ed-43b2-a1c1-205fbafe265f"}, "logfile": {"src": "hda", "id": "bf85b7bcdfa19ca1", "uuid": "38f29163-266b-48b0-9624-8bfd516f73e7"}, "__new_primary_file_unique|0.20__": {"src": "hda", "id": "eb14a43b730af9b0", "uuid": "a031af33-4cd8-4e5b-926c-a31e5bd60efc"}, "__new_primary_file_unique|0.29__": {"src": "hda", "id": "783cb8e61a95c257", "uuid": "a233e3ce-f9cb-41e7-ba68-4fbef3cc7031"}, "__new_primary_file_unique|0.38__": {"src": "hda", "id": "77520fba82154a85", "uuid": "6683bbc2-c8eb-4caa-b5c0-175565aaef41"}, "__new_primary_file_unique|0.55__": {"src": "hda", "id": "07494a3104a83c58", "uuid": "867eb8e2-805b-43b8-a020-254c764a27c4"}, "__new_primary_file_unique|0.07__": {"src": "hda", "id": "1bd4fe964f1633ec", "uuid": "3d529eea-171f-42bc-9ee7-b2b5ee04b27c"}, "__new_primary_file_unique|0.26__": {"src": "hda", "id": "c0e32004680aebdc", "uuid": "19c1897d-da47-4cbe-9aaf-a2402357915d"}, "__new_primary_file_unique|0.32__": {"src": "hda", "id": "8191b8e06b896e17", "uuid": "ff6c896b-e40b-4ba4-a214-237c1c89323c"}, "__new_primary_file_unique|0.27__": {"src": "hda", "id": "59b498d849471e88", "uuid": "20a0b8de-3faa-4698-afe3-cbf5e32ec68c"}, "__new_primary_file_unique|0.19__": {"src": "hda", "id": "713308dcadc7b298", "uuid": "81cc846e-6e1e-40ce-8928-d283c86af865"}, "__new_primary_file_unique|0.01__": {"src": "hda", "id": "94a9be080ede912f", "uuid": "2c99ebe0-181a-4ed9-a6d1-fcff02f1f95d"}, "__new_primary_file_unique|0.24__": {"src": "hda", "id": "8cd99efd35c03f63", "uuid": "df0df989-9b8f-4e8e-9656-364cbf999132"}, "__new_primary_file_unique|0.18__": {"src": "hda", "id": "098690efcaf79838", "uuid": "fea1943c-c4b0-4b4a-8939-b46a3b520e28"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(list=input_otu.dat)\nSampling 9 from 98.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.unique.subsample.dat\ninput_otu.0.01.subsample.dat\ninput_otu.0.02.subsample.dat\ninput_otu.0.03.subsample.dat\ninput_otu.0.04.subsample.dat\ninput_otu.0.05.subsample.dat\ninput_otu.0.06.subsample.dat\ninput_otu.0.07.subsample.dat\ninput_otu.0.08.subsample.dat\ninput_otu.0.09.subsample.dat\ninput_otu.0.10.subsample.dat\ninput_otu.0.11.subsample.dat\ninput_otu.0.12.subsample.dat\ninput_otu.0.13.subsample.dat\ninput_otu.0.14.subsample.dat\ninput_otu.0.15.subsample.dat\ninput_otu.0.16.subsample.dat\ninput_otu.0.17.subsample.dat\ninput_otu.0.18.subsample.dat\ninput_otu.0.19.subsample.dat\ninput_otu.0.20.subsample.dat\ninput_otu.0.21.subsample.dat\ninput_otu.0.22.subsample.dat\ninput_otu.0.23.subsample.dat\ninput_otu.0.24.subsample.dat\ninput_otu.0.25.subsample.dat\ninput_otu.0.26.subsample.dat\ninput_otu.0.27.subsample.dat\ninput_otu.0.29.subsample.dat\ninput_otu.0.32.subsample.dat\ninput_otu.0.33.subsample.dat\ninput_otu.0.36.subsample.dat\ninput_otu.0.38.subsample.dat\ninput_otu.0.41.subsample.dat\ninput_otu.0.45.subsample.dat\ninput_otu.0.55.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3303.dat' input_otu.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat &&  echo 'sub.sample( list=input_otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:35:38.794951", "params": {"count": "null", "taxonomy": "null", "dbkey": "\"hg17\"", "input": "{\"label\": null, \"use_group\": {\"to_filter\": \"no\", \"__current_case__\": 0}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3303}]}, \"__current_case__\": 1, \"format\": \"list\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "4648", "id": "25d0f693a44d3b63", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input|use_group|to_filter": "yes", "input|format": "list", "input|label": ["0.20", "0.45", "0.55"], "input|use_group|group_in": {"src": "hda", "id": "6c33be6b38ca33c8"}, "input|otu": {"src": "hda", "id": "a6914750373c5dca"}, "input|use_group|groups": ["forest", "pasture"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "a6914750373c5dca", "uuid": "273992d2-624e-4e47-9e79-53149cf7489e"}, "input|group_in": {"src": "hda", "id": "6c33be6b38ca33c8", "uuid": "4e6343ec-eef2-4ddf-870e-9f1771d9160f"}}, "update_time": "2018-02-08T18:36:06.787393", "tool_id": "mothur_sub_sample", "outputs": {"group_out": {"src": "hda", "id": "e1d9bb3f99cf6cdf", "uuid": "71c9c6f1-8226-4835-9d0e-0aac8d68b7cb"}, "__new_primary_file_0.55|0.45__": {"src": "hda", "id": "9ae55fc576dc60f1", "uuid": "47707b9a-c6e9-4112-8550-b72d078f5d33"}, "logfile": {"src": "hda", "id": "124f3cdfbbd95fda", "uuid": "14a1fcc8-3c6c-4dcb-b91b-f5f92ea6b31a"}, "__new_primary_file_0.55|0.20__": {"src": "hda", "id": "d7fb8460258b019b", "uuid": "034a36b0-49a6-4c55-a60f-4ec36e35a084"}, "__new_primary_file_0.55|0.55__": {"src": "hda", "id": "68ee566869d6b1ed", "uuid": "670a77ac-fda5-46e2-a978-5fcd0bad7785"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(list=input_otu.dat,label=0.20-0.45-0.55,group=input_use_grou \rp_group_in.dat,groups=forest-pasture,persample=false)\nSampling 9 from 98.\n0.20\n0.45\n0.55\n\nOutput File Names: \ninput_use_group_group_in.subsample.dat\ninput_otu.0.20.subsample.dat\ninput_otu.0.45.subsample.dat\ninput_otu.0.55.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3341.dat' input_otu.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3342.dat' input_use_group_group_in.dat &&  echo 'sub.sample( list=input_otu.dat ,label=0.20-0.45-0.55 ,group=input_use_group_group_in.dat ,groups=forest-pasture ,persample=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:36:03.484357", "params": {"count": "null", "taxonomy": "null", "dbkey": "\"hg17\"", "input": "{\"label\": [\"0.20\", \"0.45\", \"0.55\"], \"use_group\": {\"groups\": [\"forest\", \"pasture\"], \"group_in\": {\"values\": [{\"src\": \"hda\", \"id\": 3342}]}, \"to_filter\": \"yes\", \"__current_case__\": 1, \"persample\": \"false\"}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3341}]}, \"__current_case__\": 1, \"format\": \"list\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "4799", "id": "5d14d4d6e1b26e70", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"taxonomy": {"src": "hda", "id": "1f575f6909f01a06"}, "input|format": "fasta", "input|otu": {"src": "hda", "id": "bece6f670e32e3b2"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "1f575f6909f01a06", "uuid": "6e828b79-1871-4f06-bc3b-31124c33f80f"}, "otu": {"src": "hda", "id": "bece6f670e32e3b2", "uuid": "45d3232c-e01f-434b-baf0-a36f8911e6d7"}}, "update_time": "2018-02-08T18:36:27.157284", "tool_id": "mothur_sub_sample", "outputs": {"logfile": {"src": "hda", "id": "08fc905d422a8de9", "uuid": "50b3fb39-3176-4b2a-8d7d-56affc461bdb"}, "taxonomy_out": {"src": "hda", "id": "94b1487945e42c0e", "uuid": "ca5f7679-1915-4578-95cb-044a508074d0"}, "fasta_out": {"src": "hda", "id": "4ea647ba3b7d95df", "uuid": "071973e8-c400-49ef-b9a5-6657b427e0ae"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(fasta=input_otu.dat,taxonomy=taxonomy.dat)\nSampling 9 from 98.\n\nOutput File Names: \ntaxonomy.subsample.dat\ninput_otu.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3348.dat' input_otu.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3349.dat' taxonomy.dat && ln -s 'None' input_name_in.dat &&  echo 'sub.sample( fasta=input_otu.dat ,taxonomy=taxonomy.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:36:23.949610", "params": {"count": "null", "input": "{\"name_in\": null, \"use_group\": {\"to_filter\": \"no\", \"__current_case__\": 0}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3348}]}, \"__current_case__\": 0, \"format\": \"fasta\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "4910", "id": "3299fdcb51cc47eb", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input|use_group|to_filter": "yes", "input|format": "fasta", "input|use_group|group_in": {"src": "hda", "id": "eee039b20a991e3a"}, "input|name_in": {"src": "hda", "id": "b5720c569f7288b1"}, "input|otu": {"src": "hda", "id": "ee0ce12141350359"}, "input|use_group|groups": ["forest", "pasture"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "ee0ce12141350359", "uuid": "42469f25-5708-4222-8760-ff76e6d4d9c3"}, "name_in": {"src": "hda", "id": "b5720c569f7288b1", "uuid": "e240f77e-5836-449b-9fb9-ee9ed7a7aa34"}, "input|group_in": {"src": "hda", "id": "eee039b20a991e3a", "uuid": "a42c8f9c-d99a-48c9-a576-c8456e430272"}}, "update_time": "2018-02-08T18:36:57.127387", "tool_id": "mothur_sub_sample", "outputs": {"group_out": {"src": "hda", "id": "23aff3aec83edf3b", "uuid": "154fd6b1-2176-4bd8-ba50-bf69094a6a5d"}, "logfile": {"src": "hda", "id": "e05ecd771fc816b3", "uuid": "217b049f-b60a-4381-babb-7d066d4f80e9"}, "names_out": {"src": "hda", "id": "26cbd2176813479a", "uuid": "98e02803-23f3-4b1e-9643-8f39ea708d6a"}, "fasta_out": {"src": "hda", "id": "91ae72a932583c4d", "uuid": "3f0fd802-fd00-4559-820b-2a76a91912d9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(fasta=input_otu.dat,name=input_name_in.dat,group=input_use_g \rroup_group_in.dat,groups=forest-pasture,persample=false)\nSampling 9 from 98.\nDeconvoluting subsampled fasta file... \n/******************************************/\nRunning command: unique.seqs(fasta=input_otu.subsample.dat)\n9\t9\n\nOutput File Names: \ninput_otu.subsample.names\ninput_otu.subsample.unique.dat\n\n/******************************************/\nDone.\n\nOutput File Names: \ninput_name_in.subsample.dat\ninput_otu.subsample.dat\ninput_use_group_group_in.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3353.dat' input_otu.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3354.dat' input_name_in.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3355.dat' input_use_group_group_in.dat &&  echo 'sub.sample( fasta=input_otu.dat ,name=input_name_in.dat ,group=input_use_group_group_in.dat ,groups=forest-pasture ,persample=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:36:53.756809", "params": {"count": "null", "taxonomy": "null", "dbkey": "\"hg17\"", "input": "{\"name_in\": {\"values\": [{\"src\": \"hda\", \"id\": 3354}]}, \"use_group\": {\"groups\": [\"forest\", \"pasture\"], \"group_in\": {\"values\": [{\"src\": \"hda\", \"id\": 3355}]}, \"to_filter\": \"yes\", \"__current_case__\": 1, \"persample\": \"false\"}, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3353}]}, \"__current_case__\": 0, \"format\": \"fasta\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5043", "id": "8ef1d4aff90ec17a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"input|label": ["unique", "0.20"], "input|groups": "forest", "input|format": "shared", "input|otu": {"src": "hda", "id": "ef698126cba35364"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "ef698126cba35364", "uuid": "e59a69f6-ea54-4896-a614-6a30742cb504"}}, "update_time": "2018-02-08T18:37:24.623961", "tool_id": "mothur_sub_sample", "outputs": {"__new_primary_file_unique|0.20__": {"src": "hda", "id": "8197278eca4fd946", "uuid": "b6bbe5af-0df4-4784-b8e0-d1b94535fff7"}, "__new_primary_file_unique|unique__": {"src": "hda", "id": "3ed661d3927e064a", "uuid": "ce0d0dd6-a206-4810-9de8-2bc82dd76873"}, "logfile": {"src": "hda", "id": "85326d390990318f", "uuid": "1e3805df-515e-4e08-8f96-1e000697d674"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(shared=input_otu.dat,groups=forest,label=unique-0.20)\nSampling 49 from each group.\nunique\n0.20\n\nOutput File Names: \ninput_otu.unique.subsample.dat\ninput_otu.0.20.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3360.dat' input_otu.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat &&  echo 'sub.sample( shared=input_otu.dat ,groups=forest ,label=unique-0.20 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:37:21.465530", "params": {"count": "null", "taxonomy": "null", "dbkey": "\"hg17\"", "input": "{\"groups\": \"forest\", \"label\": [\"unique\", \"0.20\"], \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3360}]}, \"__current_case__\": 2, \"format\": \"shared\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5144", "id": "28ff0d67f20f4379", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"input|format": "rabund", "input|otu": {"src": "hda", "id": "edee4d329f8f498b"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "edee4d329f8f498b", "uuid": "d7a3be04-025a-4ede-a135-079084fb394f"}}, "update_time": "2018-02-08T18:37:42.101206", "tool_id": "mothur_sub_sample", "outputs": {"rabund_out": {"src": "hda", "id": "d7f196f58f1b0b71", "uuid": "d6cfb504-3504-4392-bf5e-7afcb080ec67"}, "logfile": {"src": "hda", "id": "46e41148fd1dda0c", "uuid": "011d4c74-d116-42a0-b8a6-a250368b8f9a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(rabund=input_otu.dat)\nSampling 9 from 98.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3364.dat' input_otu.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat &&  echo 'sub.sample( rabund=input_otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:37:38.974213", "params": {"count": "null", "taxonomy": "null", "dbkey": "\"hg17\"", "input": "{\"label\": null, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3364}]}, \"__current_case__\": 4, \"format\": \"rabund\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5235", "id": "45a4f11c8f7e7223", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000005", "has_data": true}, {"data": {"status": "success", "inputs": {"input|format": "sabund", "input|otu": {"src": "hda", "id": "10d4ec46a6dab525"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "10d4ec46a6dab525", "uuid": "485908f3-8e8b-4984-a10e-f9718499bf14"}}, "update_time": "2018-02-08T18:37:59.562528", "tool_id": "mothur_sub_sample", "outputs": {"sabund_out": {"src": "hda", "id": "edb9aecf4037cd61", "uuid": "844b4d73-8677-45ee-93cf-9da60b83311f"}, "logfile": {"src": "hda", "id": "78353c3ca164fa23", "uuid": "30f65e57-bb1f-4dbb-9cfe-e552341c898a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > sub.sample(sabund=input_otu.dat)\nSampling 9 from 98.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.subsample.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3367.dat' input_otu.dat && ln -s 'None' count.dat && ln -s 'None' taxonomy.dat &&  echo 'sub.sample( sabund=input_otu.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:37:56.411698", "params": {"count": "null", "taxonomy": "null", "dbkey": "\"hg17\"", "input": "{\"label\": null, \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3367}]}, \"__current_case__\": 3, \"format\": \"sabund\"}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5329", "id": "973cca1598618f36", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_sub_sample.test_tool_000006", "has_data": true}, {"data": {"status": "success", "inputs": {"qfile": {"src": "hda", "id": "997fdd605baf4477"}}, "job": {"inputs": {"qfile": {"src": "hda", "id": "997fdd605baf4477", "uuid": "b13158ea-6190-42e6-a8ae-3a5c21ead029"}}, "update_time": "2018-02-08T18:38:17.046071", "tool_id": "mothur_summary_qual", "outputs": {"logfile": {"src": "hda", "id": "be79454c845000eb", "uuid": "75a6e837-a714-412f-8804-367ca29718e0"}, "out_summary": {"src": "hda", "id": "c4be6070688ee40e", "uuid": "b3c138ce-bf0f-42a9-827e-bd29523e12e1"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.qual(qfile=qfile.dat)\n\nUsing 1 processors.\n\nPosition\tNumSeqs\tAverageQ\n0\t25\t31.760000\n100\t25\t29.719999\n200\t25\t28.799999\n\nIt took 0 secs to create the summary file for 25 sequences.\n\n\nOutput File Names: \nqfile.qual.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3370.dat' qfile.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'summary.qual( qfile=qfile.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:38:13.919763", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5418", "id": "76bb1b91489711f4", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_qual.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "56ac79356c05acc8"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "56ac79356c05acc8", "uuid": "6f0d83d5-f9ac-46f9-9ace-50ad5ceeb974"}}, "update_time": "2018-02-08T18:38:29.506638", "tool_id": "mothur_summary_seqs", "outputs": {"logfile": {"src": "hda", "id": "d5f96994fda893d3", "uuid": "75fbfa36-0d67-4a1f-abbe-68f632470429"}, "out_summary": {"src": "hda", "id": "08a03081f5d556bd", "uuid": "cef79172-0f84-4dc6-a21a-226ca0d18391"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.seqs(fasta=fasta.dat,processors=1)\n\nUsing 1 processors.\n\n\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs\nMinimum:\t1\t252\t252\t0\t3\t1\n2.5%-tile:\t1\t252\t252\t0\t3\t1\n25%-tile:\t1\t253\t253\t0\t4\t7\nMedian: \t1\t253\t253\t0\t4\t13\n75%-tile:\t1\t253\t253\t0\t5\t19\n97.5%-tile:\t1\t254\t254\t8\t6\t25\nMaximum:\t1\t254\t254\t8\t6\t25\nMean:\t1\t252.92\t252.92\t0.4\t4.24\n# of Seqs:\t25\n\nOutput File Names: \nfasta.summary\n\nIt took 0 secs to summarize 25 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3373.dat' fasta.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'summary.seqs( fasta=fasta.dat, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:38:26.369792", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5507", "id": "40537184298763b3", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "bfbf916ea0862825"}, "name": {"src": "hda", "id": "a1bca696e6338746"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "bfbf916ea0862825", "uuid": "441d697c-304b-48b5-b977-c692f16ebf90"}, "name": {"src": "hda", "id": "a1bca696e6338746", "uuid": "fd30122b-1410-4d81-a9c9-06d3623f37cf"}}, "update_time": "2018-02-08T18:38:50.021600", "tool_id": "mothur_summary_seqs", "outputs": {"logfile": {"src": "hda", "id": "d308ef85a2ecdd63", "uuid": "8d77bc24-c3a9-476a-a08f-88dcc3f16174"}, "out_summary": {"src": "hda", "id": "bd5984605556083f", "uuid": "97a18d25-524f-41a4-9f71-b5db69e2a367"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.seqs(fasta=fasta.dat,name=name.dat,processors=1)\n\nUsing 1 processors.\n\n\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs\nMinimum:\t1\t422\t422\t0\t4\t1\n2.5%-tile:\t1\t436\t436\t0\t4\t3\n25%-tile:\t1\t507\t507\t1\t5\t25\nMedian: \t1\t530\t530\t3\t5\t50\n75%-tile:\t1\t961\t961\t6\t6\t74\n97.5%-tile:\t1\t973\t973\t15\t8\t96\nMaximum:\t1\t978\t978\t20\t9\t98\nMean:\t1\t678.235\t678.235\t4.54082\t5.44898\n# of unique seqs:\t96\ntotal # of seqs:\t98\n\nOutput File Names: \nfasta.summary\n\nIt took 0 secs to summarize 98 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3376.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3377.dat' name.dat && ln -s 'None' count.dat &&  echo 'summary.seqs( fasta=fasta.dat, name=name.dat, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:38:46.918829", "params": {"count": "null", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5627", "id": "0cc52239f966e8d8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "d32f8d2680587f70"}, "fasta": {"src": "hda", "id": "561fb224c4db80ce"}}, "job": {"inputs": {"count": {"src": "hda", "id": "d32f8d2680587f70", "uuid": "89db742d-5a41-4b17-8121-7d7990cac273"}, "fasta": {"src": "hda", "id": "561fb224c4db80ce", "uuid": "82f53e55-3751-4359-9711-7e6d49e40902"}}, "update_time": "2018-02-08T18:39:10.818528", "tool_id": "mothur_summary_seqs", "outputs": {"logfile": {"src": "hda", "id": "183b6b1fd8567283", "uuid": "f98a65a4-a5af-44c6-901d-c2870b7e17a4"}, "out_summary": {"src": "hda", "id": "309dfc9ec023321e", "uuid": "88e59858-87d0-4485-813c-2060acf87822"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.seqs(fasta=fasta.dat,count=count.dat,processors=1)\n\nUsing 1 processors.\n\n\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs\nMinimum:\t1\t422\t422\t0\t4\t1\n2.5%-tile:\t1\t436\t436\t0\t4\t3\n25%-tile:\t1\t507\t507\t1\t5\t25\nMedian: \t1\t530\t530\t3\t5\t50\n75%-tile:\t1\t961\t961\t6\t6\t74\n97.5%-tile:\t1\t973\t973\t15\t8\t96\nMaximum:\t1\t978\t978\t20\t9\t98\nMean:\t1\t678.235\t678.235\t4.54082\t5.44898\n# of unique seqs:\t96\ntotal # of seqs:\t98\n\nOutput File Names: \nfasta.summary\n\nIt took 0 secs to summarize 98 sequences.\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3380.dat' fasta.dat && ln -s 'None' name.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3381.dat' count.dat &&  echo 'summary.seqs( fasta=fasta.dat, count=count.dat, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:39:07.731295", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "name": "null", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5738", "id": "20daa85480c5e233", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "0426109cd781ead0"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "0426109cd781ead0", "uuid": "bdb3a54a-e140-44c2-9d09-1eea16f2634a"}}, "update_time": "2018-02-08T18:39:28.523455", "tool_id": "mothur_summary_shared", "outputs": {"logfile": {"src": "hda", "id": "66e1b7e2cc1eadad", "uuid": "98586141-b915-4211-8008-76ce467ce6fa"}, "summary": {"src": "hda", "id": "3cd2bed6e83f9950", "uuid": "59846e5d-4dc2-4cfb-9db0-7d6977934fe4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.shared(shared=otu.dat,calc=sharedsobs-sharedchao-sharedace-jcla \rss-jest-sorclass-sorest-jabund-sorabund-thetan-thetayc,all=false,distance=false, \routput=lt,processors=1)\n\nUsing 1 processors.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3384.dat' otu.dat &&  echo 'summary.shared( shared=otu.dat, calc=sharedsobs-sharedchao-sharedace-jclass-jest-sorclass-sorest-jabund-sorabund-thetan-thetayc, all=false, distance=false, output=lt, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:39:25.392601", "params": {"distance": "\"false\"", "all": "\"false\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"use\": \"no\", \"__current_case__\": 1}", "groups": "null", "output": "\"lt\"", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"jclass\", \"jest\", \"sorclass\", \"sorest\", \"jabund\", \"sorabund\", \"thetan\", \"thetayc\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5829", "id": "68b1b014e79dbbac", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"subsample|use": "yes", "otu": {"src": "hda", "id": "254a819efefe8354"}, "subsample|iters": "42", "subsample|subsample": "10"}, "job": {"inputs": {"otu": {"src": "hda", "id": "254a819efefe8354", "uuid": "aaf98054-0ba0-481b-91bf-9da58d5967e4"}}, "update_time": "2018-02-08T18:39:46.006201", "tool_id": "mothur_summary_shared", "outputs": {"logfile": {"src": "hda", "id": "cded715b2eb96d19", "uuid": "daa6c625-e03b-4735-8b46-013ba527ad23"}, "summary": {"src": "hda", "id": "c6fdefa03add2afa", "uuid": "95ec8fed-62b1-4cc9-8287-621a7afac31e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.shared(shared=otu.dat,calc=sharedsobs-sharedchao-sharedace-jcla \rss-jest-sorclass-sorest-jabund-sorabund-thetan-thetayc,all=false,distance=false, \rsubsample=10,iters=42,output=lt,processors=1)\n\nUsing 1 processors.\n0.10\n\nOutput File Names: \notu.summary\notu.sharedsobs.0.10.lt.dist\notu.sharedchao.0.10.lt.dist\notu.sharedace.0.10.lt.dist\notu.jclass.0.10.lt.dist\notu.jest.0.10.lt.dist\notu.sorclass.0.10.lt.dist\notu.sorest.0.10.lt.dist\notu.jabund.0.10.lt.dist\notu.sorabund.0.10.lt.dist\notu.thetan.0.10.lt.dist\notu.thetayc.0.10.lt.dist\notu.sharedsobs.0.10.lt.ave.dist\notu.sharedsobs.0.10.lt.std.dist\notu.sharedchao.0.10.lt.ave.dist\notu.sharedchao.0.10.lt.std.dist\notu.sharedace.0.10.lt.ave.dist\notu.sharedace.0.10.lt.std.dist\notu.jclass.0.10.lt.ave.dist\notu.jclass.0.10.lt.std.dist\notu.jest.0.10.lt.ave.dist\notu.jest.0.10.lt.std.dist\notu.sorclass.0.10.lt.ave.dist\notu.sorclass.0.10.lt.std.dist\notu.sorest.0.10.lt.ave.dist\notu.sorest.0.10.lt.std.dist\notu.jabund.0.10.lt.ave.dist\notu.jabund.0.10.lt.std.dist\notu.sorabund.0.10.lt.ave.dist\notu.sorabund.0.10.lt.std.dist\notu.thetan.0.10.lt.ave.dist\notu.thetan.0.10.lt.std.dist\notu.thetayc.0.10.lt.ave.dist\notu.thetayc.0.10.lt.std.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3387.dat' otu.dat &&  echo 'summary.shared( shared=otu.dat, calc=sharedsobs-sharedchao-sharedace-jclass-jest-sorclass-sorest-jabund-sorabund-thetan-thetayc, all=false, distance=false, subsample=10, iters=42, output=lt, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:39:42.829423", "params": {"distance": "\"false\"", "all": "\"false\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"iters\": \"42\", \"subsample\": \"10\", \"use\": \"yes\", \"__current_case__\": 0}", "groups": "null", "output": "\"lt\"", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"jclass\", \"jest\", \"sorclass\", \"sorest\", \"jabund\", \"sorabund\", \"thetan\", \"thetayc\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "5925", "id": "71eba17e79d46ea5", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"calc": ["sharedsobs", "sharedchao", "sharedace", "anderberg", "jclass", "jest", "kulczynski", "kulczynskicody", "kstest", "lennon", "ochiai", "sorclass", "sorest", "whittaker", "hamming", "memchi2", "memchord", "memeuclidean", "mempearson", "braycurtis", "jabund", "morisitahorn", "sorabund", "thetan", "thetayc", "canberra", "gower", "hellinger", "manhattan", "odum", "soergel", "spearman", "speciesprofile", "structchi2", "structchord", "structeuclidean", "structkulczynski", "structpearson", "sharednseqs", "sharedobserved"], "otu": {"src": "hda", "id": "e747dd9ffcf57168"}, "groups": ["forest", "pasture"], "label": ["0.05", "0.22", "0.32"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "e747dd9ffcf57168", "uuid": "59d81e55-859a-492b-aa87-40e647394b7e"}}, "update_time": "2018-02-08T18:40:03.413375", "tool_id": "mothur_summary_shared", "outputs": {"logfile": {"src": "hda", "id": "75d696f5e8005428", "uuid": "d3c6f0a0-fa22-4672-94c1-da0bf5ab2f46"}, "summary": {"src": "hda", "id": "da7a9cd1bf67613c", "uuid": "d24a67fa-9b8b-4683-becf-e5e71f369043"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.shared(shared=otu.dat,label=0.05-0.22-0.32,groups=forest-pastur \re,calc=sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczyns \rkicody-kstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-m \remeuclidean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-ca \rnberra-gower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-structchi2 \r-structchord-structeuclidean-structkulczynski-structpearson-sharednseqs-sharedob \rserved,all=false,distance=false,output=lt,processors=1)\n\nUsing 1 processors.\nsharedobserved is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are anderberg, braycurtis, canberra, default, gower, hamming, hellinger, jabund, jclass, jest, jsd, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, rjsd, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker, \n0.05\n0.22\n0.32\n\nOutput File Names: \notu.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3390.dat' otu.dat &&  echo 'summary.shared( shared=otu.dat, label=0.05-0.22-0.32, groups=forest-pasture, calc=sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-kstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-memeuclidean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-canberra-gower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-structchi2-structchord-structeuclidean-structkulczynski-structpearson-sharednseqs-sharedobserved, all=false, distance=false, output=lt, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:40:00.489517", "params": {"distance": "\"false\"", "all": "\"false\"", "dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.22\", \"0.32\"]", "subsample": "{\"use\": \"no\", \"__current_case__\": 1}", "groups": "[\"forest\", \"pasture\"]", "output": "\"lt\"", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"anderberg\", \"jclass\", \"jest\", \"kulczynski\", \"kulczynskicody\", \"kstest\", \"lennon\", \"ochiai\", \"sorclass\", \"sorest\", \"whittaker\", \"hamming\", \"memchi2\", \"memchord\", \"memeuclidean\", \"mempearson\", \"braycurtis\", \"jabund\", \"morisitahorn\", \"sorabund\", \"thetan\", \"thetayc\", \"canberra\", \"gower\", \"hellinger\", \"manhattan\", \"odum\", \"soergel\", \"spearman\", \"speciesprofile\", \"structchi2\", \"structchord\", \"structeuclidean\", \"structkulczynski\", \"structpearson\", \"sharednseqs\", \"sharedobserved\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6045", "id": "617cf9f340bd6e86", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_shared.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"distance": true, "calc": "sorclass", "otu": {"src": "hda", "id": "b443405669a58394"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "b443405669a58394", "uuid": "9c2927b2-b6be-4c3d-9f35-e3ffb0ed545c"}}, "update_time": "2018-02-08T18:40:22.695570", "tool_id": "mothur_summary_shared", "outputs": {"__new_primary_file_sorclass.unique.lt|sorclass.0.20.lt__": {"src": "hda", "id": "c6b272724420a0c3", "uuid": "c3c3c914-e794-404a-8ae6-c5f927315eb3"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.16.lt__": {"src": "hda", "id": "fbf13bbace0e382f", "uuid": "ced285e3-693a-4653-8054-29c1e871b8c8"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.38.lt__": {"src": "hda", "id": "a9b933fa687d9518", "uuid": "d34cfb4c-ae40-41e5-8925-4955c6f0d4b7"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.41.lt__": {"src": "hda", "id": "5a3d96751cec6e3e", "uuid": "4446d774-e6cc-44d6-92a3-17aa2eb4a61e"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.15.lt__": {"src": "hda", "id": "7b9f8b98c4ffad77", "uuid": "7516dc4e-4037-4c88-9afd-cf7ff670952e"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.12.lt__": {"src": "hda", "id": "3282233258f0f7fb", "uuid": "fc7b66ab-3c8a-4ab3-9496-ba84db2f0731"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.08.lt__": {"src": "hda", "id": "549fe069f41f5e42", "uuid": "365bffa5-59d1-44fa-b958-25b05b357828"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.11.lt__": {"src": "hda", "id": "feb74fd2f7fd44fb", "uuid": "5537588f-6aa0-4c34-86b9-bcac45e7c8ef"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.36.lt__": {"src": "hda", "id": "6c0029535d6b5111", "uuid": "1aaea491-b9b1-4052-b65a-c98cfab6ed52"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.33.lt__": {"src": "hda", "id": "fca77c5af4471e3e", "uuid": "e9edeb83-266d-4fe6-8160-86a967b21ddb"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.25.lt__": {"src": "hda", "id": "710299148e65bdb4", "uuid": "db0a5fc7-2f8d-4eb4-9dc2-e57635ca41ab"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.19.lt__": {"src": "hda", "id": "1e9f3a99da895dd5", "uuid": "08b73e49-5643-466c-86c6-23ce58861812"}, "__new_primary_file_sorclass.unique.lt|sorclass.unique.lt__": {"src": "hda", "id": "fc51f4aebb0d65c0", "uuid": "8fa6fbcb-a7f8-4800-a968-a4911976e902"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.32.lt__": {"src": "hda", "id": "bec9e7f6333d2f36", "uuid": "156b9944-86bc-45ef-ac41-9d5291dd252d"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.26.lt__": {"src": "hda", "id": "bf875c8c7ae3c4c1", "uuid": "90d2df26-0a4e-4e6d-ac1c-81cb840c3761"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.03.lt__": {"src": "hda", "id": "9e4763fe06d09ee1", "uuid": "cebd135c-c029-42e4-8a13-edcf9f7fa2a8"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.04.lt__": {"src": "hda", "id": "a3a91b9854e528c1", "uuid": "8c3d70ea-ac21-4191-9e66-60bb499d8e46"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.14.lt__": {"src": "hda", "id": "6b308095f18dba3b", "uuid": "9ba48b4e-d989-467d-adfb-5583f91b0f62"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.01.lt__": {"src": "hda", "id": "d0f92696983585f3", "uuid": "3836c464-9fa2-42ab-8f7a-98eeae340704"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.18.lt__": {"src": "hda", "id": "b97c4dee7d66e350", "uuid": "beca01d7-5288-44c6-ba13-8d6bce14c1fc"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.09.lt__": {"src": "hda", "id": "c57e8cad56a6ff2a", "uuid": "cfc4ffbc-8b06-4608-9448-6e8bdbbee96a"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.29.lt__": {"src": "hda", "id": "49b04723a575686c", "uuid": "efac65e1-b627-4685-960b-021dc4682f49"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.22.lt__": {"src": "hda", "id": "10b3c1fe38490935", "uuid": "d7be3e40-f86a-41e5-9cbd-bebc6ca8a987"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.21.lt__": {"src": "hda", "id": "30b2b5ef7167ced6", "uuid": "50d3ac63-53e2-43bd-966c-0dbf3b34fa53"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.05.lt__": {"src": "hda", "id": "8031952532462a13", "uuid": "d9dfc3e0-370d-42a5-a4b9-a7fc39506fab"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.23.lt__": {"src": "hda", "id": "0dea4abf9bb0415a", "uuid": "c692dc6d-b5db-4d53-a90d-d7f162177c91"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.02.lt__": {"src": "hda", "id": "5936ec972cea4795", "uuid": "0a08ca9f-39b2-44b1-a5f4-f422a557ddb3"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.06.lt__": {"src": "hda", "id": "4efb683e59835243", "uuid": "ff63daba-f9ac-495b-9c99-004a47c23bc6"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.27.lt__": {"src": "hda", "id": "777dd7569c196c76", "uuid": "956fcdce-a6d3-4d84-b713-c35ab476121b"}, "logfile": {"src": "hda", "id": "10212f8402b2f379", "uuid": "93761f5c-938e-46a6-adcb-511c4a7d4032"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.45.lt__": {"src": "hda", "id": "0d3149843a425eae", "uuid": "ed2d13b5-f26e-454d-86a4-956bcea163d6"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.24.lt__": {"src": "hda", "id": "bfd4ea23a1e8bbdd", "uuid": "b2d06a53-2ec3-4e5b-be3c-6a27f2d87d0f"}, "summary": {"src": "hda", "id": "8747915bc2bfc819", "uuid": "05e4e93c-2242-4fff-85b0-37eebcd5fd19"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.13.lt__": {"src": "hda", "id": "5fc0b50ca858f8c5", "uuid": "95c1eeb0-1d07-468a-a70a-883db948f832"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.10.lt__": {"src": "hda", "id": "f8ccb799d73ec3dd", "uuid": "548923ee-863b-4120-a0dd-2d27df2d49c2"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.17.lt__": {"src": "hda", "id": "74bd528cdd946582", "uuid": "c3f23ca4-9d84-4027-9dc2-e7f85a80fcd7"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.07.lt__": {"src": "hda", "id": "f241b8715eaa6b7a", "uuid": "e60417f2-c85b-4b50-ae86-feb13f49d5a5"}, "__new_primary_file_sorclass.unique.lt|sorclass.0.55.lt__": {"src": "hda", "id": "af41e4fac73960a1", "uuid": "90ea88dc-ea36-4b42-a782-e4d6556864b8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.shared(shared=otu.dat,calc=sorclass,all=false,distance=true,out \rput=lt,processors=1)\n\nUsing 1 processors.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.summary\notu.sorclass.unique.lt.dist\notu.sorclass.0.01.lt.dist\notu.sorclass.0.02.lt.dist\notu.sorclass.0.03.lt.dist\notu.sorclass.0.04.lt.dist\notu.sorclass.0.05.lt.dist\notu.sorclass.0.06.lt.dist\notu.sorclass.0.07.lt.dist\notu.sorclass.0.08.lt.dist\notu.sorclass.0.09.lt.dist\notu.sorclass.0.10.lt.dist\notu.sorclass.0.11.lt.dist\notu.sorclass.0.12.lt.dist\notu.sorclass.0.13.lt.dist\notu.sorclass.0.14.lt.dist\notu.sorclass.0.15.lt.dist\notu.sorclass.0.16.lt.dist\notu.sorclass.0.17.lt.dist\notu.sorclass.0.18.lt.dist\notu.sorclass.0.19.lt.dist\notu.sorclass.0.20.lt.dist\notu.sorclass.0.21.lt.dist\notu.sorclass.0.22.lt.dist\notu.sorclass.0.23.lt.dist\notu.sorclass.0.24.lt.dist\notu.sorclass.0.25.lt.dist\notu.sorclass.0.26.lt.dist\notu.sorclass.0.27.lt.dist\notu.sorclass.0.29.lt.dist\notu.sorclass.0.32.lt.dist\notu.sorclass.0.33.lt.dist\notu.sorclass.0.36.lt.dist\notu.sorclass.0.38.lt.dist\notu.sorclass.0.41.lt.dist\notu.sorclass.0.45.lt.dist\notu.sorclass.0.55.lt.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3393.dat' otu.dat &&  echo 'summary.shared( shared=otu.dat, calc=sorclass, all=false, distance=true, output=lt, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:40:17.726109", "params": {"distance": "\"true\"", "all": "\"false\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"use\": \"no\", \"__current_case__\": 1}", "groups": "null", "output": "\"lt\"", "calc": "\"sorclass\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6135", "id": "e033f1f6a16a5fdb", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_shared.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "bcc40440bc682f91"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "bcc40440bc682f91", "uuid": "cfb793d1-0a5b-4fb0-8348-342f73d77406"}}, "update_time": "2018-02-08T18:40:47.563664", "tool_id": "mothur_summary_single", "outputs": {"subsample_summary": {"src": "hda", "id": "8223d3aea03f91a3", "uuid": "5013c585-03ac-4702-934b-1120f0e54c2b"}, "logfile": {"src": "hda", "id": "a8b76ec0d8bb9cbb", "uuid": "0121e22c-dc77-450e-b2b8-d470c1e949cd"}, "summary": {"src": "hda", "id": "e75c6e7fd38a1506", "uuid": "498bcf3f-59f1-4df3-9878-5b7e881d6eef"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.single(shared=otu.dat,groupmode=true,calc=ace-chao-jack-sobs-si \rmpson-shannon-npshannon,abund=10)\n\nProcessing group forest\n\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nProcessing group pasture\n\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.groups.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3432.dat' otu.dat &&  echo 'summary.single( shared=otu.dat, groupmode=true ,calc=ace-chao-jack-sobs-simpson-shannon-npshannon ,abund=10 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:40:44.372596", "params": {"abund": "\"10\"", "groupmode": "\"true\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"use\": \"no\", \"__current_case__\": 1}", "calc": "[\"ace\", \"chao\", \"jack\", \"sobs\", \"simpson\", \"shannon\", \"npshannon\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6237", "id": "f691a5951523571b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_single.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"calc": ["ace", "bootstrap", "chao", "jack", "sobs", "simpsoneven", "shannoneven", "heip", "smithwilson", "bergerparker", "coverage", "goodscoverage", "simpson", "invsimpson", "qstat", "shannon", "npshannon", "boneh", "efron", "shen", "solow", "logseries", "geometric", "bstick", "nseqs"], "otu": {"src": "hda", "id": "7d4fdaa4731a0a66"}, "label": ["0.05", "0.22", "0.32"]}, "job": {"inputs": {"otu": {"src": "hda", "id": "7d4fdaa4731a0a66", "uuid": "d335fa95-0e14-4417-ac8d-7dda122edf81"}}, "update_time": "2018-02-08T18:41:05.019830", "tool_id": "mothur_summary_single", "outputs": {"subsample_summary": {"src": "hda", "id": "7058e5df1feb4870", "uuid": "6677b51b-6194-4588-9305-54a602c6e0d8"}, "logfile": {"src": "hda", "id": "3c8c6806cad72b43", "uuid": "98646530-a51f-40f7-bfe0-dfb9c1d72bd1"}, "summary": {"src": "hda", "id": "97e0cfb4245121c2", "uuid": "a6b1aaa8-0a10-4db0-9562-c5b664054a9e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.single(shared=otu.dat,groupmode=true,label=0.05-0.22-0.32,calc= \race-bootstrap-chao-jack-sobs-simpsoneven-shannoneven-heip-smithwilson-bergerpark \rer-coverage-goodscoverage-simpson-invsimpson-qstat-shannon-npshannon-boneh-efron \r-shen-solow-logseries-geometric-bstick-nseqs,abund=10)\n\nProcessing group forest\n\n0.05\n0.22\n0.32\n\nProcessing group pasture\n\n0.05\n0.22\n0.32\n\nOutput File Names: \notu.groups.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3436.dat' otu.dat &&  echo 'summary.single( shared=otu.dat, groupmode=true ,label=0.05-0.22-0.32 ,calc=ace-bootstrap-chao-jack-sobs-simpsoneven-shannoneven-heip-smithwilson-bergerparker-coverage-goodscoverage-simpson-invsimpson-qstat-shannon-npshannon-boneh-efron-shen-solow-logseries-geometric-bstick-nseqs ,abund=10 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:41:01.859227", "params": {"abund": "\"10\"", "groupmode": "\"true\"", "dbkey": "\"hg17\"", "label": "[\"0.05\", \"0.22\", \"0.32\"]", "subsample": "{\"use\": \"no\", \"__current_case__\": 1}", "calc": "[\"ace\", \"bootstrap\", \"chao\", \"jack\", \"sobs\", \"simpsoneven\", \"shannoneven\", \"heip\", \"smithwilson\", \"bergerparker\", \"coverage\", \"goodscoverage\", \"simpson\", \"invsimpson\", \"qstat\", \"shannon\", \"npshannon\", \"boneh\", \"efron\", \"shen\", \"solow\", \"logseries\", \"geometric\", \"bstick\", \"nseqs\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6322", "id": "824db84bb730ff40", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_single.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"otu": {"src": "hda", "id": "046dc814339ceff4"}, "groupmode": false}, "job": {"inputs": {"otu": {"src": "hda", "id": "046dc814339ceff4", "uuid": "5d866346-b6e2-40e8-aa7f-21a7a7ca52b8"}}, "update_time": "2018-02-08T18:41:22.364406", "tool_id": "mothur_summary_single", "outputs": {"__new_primary_file_pasture|forest__": {"src": "hda", "id": "10280f41f2c7c752", "uuid": "280db29e-fa14-46cb-b8eb-b36a5103e501"}, "logfile": {"src": "hda", "id": "7ecd6e9675e139a5", "uuid": "c199174e-86c5-4c48-929e-045952aea5da"}, "__new_primary_file_pasture|pasture__": {"src": "hda", "id": "09457d21386fcba3", "uuid": "134660e0-0e9f-41d3-8967-863d43c77492"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.single(shared=otu.dat,groupmode=false,calc=ace-chao-jack-sobs-s \rimpson-shannon-npshannon,abund=10)\n\nProcessing group forest\n\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nProcessing group pasture\n\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.forest.summary\notu.pasture.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3440.dat' otu.dat &&  echo 'summary.single( shared=otu.dat, groupmode=false ,calc=ace-chao-jack-sobs-simpson-shannon-npshannon ,abund=10 )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:41:19.336102", "params": {"abund": "\"10\"", "groupmode": "\"false\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"use\": \"no\", \"__current_case__\": 1}", "calc": "[\"ace\", \"chao\", \"jack\", \"sobs\", \"simpson\", \"shannon\", \"npshannon\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6407", "id": "030656b247de0efe", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_single.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"subsample|use": "yes", "otu": {"src": "hda", "id": "637ab171f9780706"}, "subsample|iters": "42", "subsample|subsample": "10"}, "job": {"inputs": {"otu": {"src": "hda", "id": "637ab171f9780706", "uuid": "50d44bc0-2460-415c-b57b-6488b6c68d87"}}, "update_time": "2018-02-08T18:41:39.911044", "tool_id": "mothur_summary_single", "outputs": {"subsample_summary": {"src": "hda", "id": "bd8bdd2a2038a190", "uuid": "153e4833-9b1e-4ebb-9b30-3edeb40fd930"}, "logfile": {"src": "hda", "id": "7822d21d2c1efd0f", "uuid": "6e7de8a6-23f3-48b9-a297-f29da3fa89e3"}, "summary": {"src": "hda", "id": "1bf84afd7b930518", "uuid": "ab83ce62-5f57-4e0c-b7e4-e6a3017d55a6"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.single(rabund=otu.dat,calc=ace-chao-jack-sobs-simpson-shannon-n \rpshannon,abund=10,subsample=10,iters=42)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \notu.summary\notu.ave_std.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3444.dat' otu.dat &&  echo 'summary.single( rabund=otu.dat ,calc=ace-chao-jack-sobs-simpson-shannon-npshannon ,abund=10 ,subsample=10 ,iters=42 )' | sed 's/ //g' | mothur | tee mothur.out.log && mv otu.*ave_std.summary otu.ave-std", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:41:36.674896", "params": {"abund": "\"10\"", "groupmode": "\"true\"", "dbkey": "\"hg17\"", "label": "null", "subsample": "{\"iters\": \"42\", \"subsample\": \"10\", \"use\": \"yes\", \"__current_case__\": 0}", "calc": "[\"ace\", \"chao\", \"jack\", \"sobs\", \"simpson\", \"shannon\", \"npshannon\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "size": "\"\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6495", "id": "35610b944eae1662", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_single.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"tax|source": "hist", "tax|taxonomy": {"src": "hda", "id": "97f081ffc622334b"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "97f081ffc622334b", "uuid": "94641a0d-5fcd-4a33-9735-80ca65bbce70"}}, "update_time": "2018-02-08T18:42:02.367553", "tool_id": "mothur_summary_tax", "outputs": {"logfile": {"src": "hda", "id": "ef827ef9990b2a18", "uuid": "637cc626-75b4-4632-8123-48e27a7d16d9"}, "taxsummary": {"src": "hda", "id": "13bed055b69c3f53", "uuid": "013032a7-b3f4-4148-b0c5-5d9301e501f5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.tax(taxonomy=tax.taxonomy.dat,relabund=false)\n\nIt took 0 secs to create the summary file for 242 sequences.\n\n\nOutput File Names: \ntax.taxonomy.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3448.dat' tax.taxonomy.dat && ln -s 'None' name.dat && ln -s 'None' group.dat && ln -s 'None' count.dat &&  echo 'summary.tax( taxonomy=tax.taxonomy.dat, relabund=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:41:59.440341", "params": {"count": "null", "group": "null", "name": "null", "relabund": "\"false\"", "tax": "{\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 3448}]}}", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6584", "id": "0f7bfbeda1808692", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_tax.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"tax|source": "hist", "tax|taxonomy": {"src": "hda", "id": "5703175d6b845ade"}}, "job": {"inputs": {"taxonomy": {"src": "hda", "id": "5703175d6b845ade", "uuid": "523cfa41-689b-48c1-84d2-c6b4b8fabf74"}}, "update_time": "2018-02-08T18:42:19.745721", "tool_id": "mothur_summary_tax", "outputs": {"logfile": {"src": "hda", "id": "a062654a409016a9", "uuid": "afd4ff3b-f29e-4de1-b3ad-9effa990ef5b"}, "taxsummary": {"src": "hda", "id": "498b124981096150", "uuid": "7794df82-88d4-4f07-a14c-5237fa5da76a"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > summary.tax(taxonomy=tax.taxonomy.dat,relabund=false)\n\nIt took 0 secs to create the summary file for 242 sequences.\n\n\nOutput File Names: \ntax.taxonomy.tax.summary\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3451.dat' tax.taxonomy.dat && ln -s 'None' name.dat && ln -s 'None' group.dat && ln -s 'None' count.dat &&  echo 'summary.tax( taxonomy=tax.taxonomy.dat, relabund=false )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:42:16.663062", "params": {"count": "null", "group": "null", "name": "null", "relabund": "\"false\"", "tax": "{\"source\": \"hist\", \"__current_case__\": 1, \"taxonomy\": {\"values\": [{\"src\": \"hda\", \"id\": 3451}]}}", "dbkey": "\"hg17\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6673", "id": "32e4cd7ce068c585", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_summary_tax.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input|dist": {"src": "hda", "id": "6201901e7bcadfb4"}, "input|source": "phylip"}, "job": {"inputs": {"dist": {"src": "hda", "id": "6201901e7bcadfb4", "uuid": "62a2698a-0ed3-4ecb-8d7d-3a9ac80d514e"}}, "update_time": "2018-02-08T18:42:37.247942", "tool_id": "mothur_tree_shared", "outputs": {"logfile": {"src": "hda", "id": "231281dccddcf77b", "uuid": "d331c62c-2528-404b-8d3e-fae0d559cbb2"}, "tre": {"src": "hda", "id": "bcdc79e6d8f62c6d", "uuid": "3b6a726e-e127-40bb-b982-64d8d017cb9b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > tree.shared(phylip=input_dist.dat,calc=jclass-thetayc,processors=1)\n\nUsing 1 processors.\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\nTree complete. \n\nOutput File Names: \ninput_dist.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3454.dat' input_dist.dat && ln -s 'None' input_name.dat &&  echo 'tree.shared( phylip=input_dist.dat, calc=jclass-thetayc, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:42:34.145621", "params": {"input": "{\"source\": \"phylip\", \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 3454}]}, \"name\": null, \"__current_case__\": 1}", "calc": "[\"jclass\", \"thetayc\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6772", "id": "d1ff5636c3d156c1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_tree_shared.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"input|subsampling|use": 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"uuid": "25c46b16-8b69-4209-9039-608684d18c03"}, "__new_primary_file_jclass.unique.cons|jclass.0.38.ave__": {"src": "hda", "id": "f1ffd5138cc4a01d", "uuid": "474884c6-2d98-4793-834f-4fbf5d185cfb"}, "__new_primary_file_jclass.unique.cons|jclass.0.01.ave__": {"src": "hda", "id": "583e03b410a3a90a", "uuid": "10f34357-ee4b-40e7-b505-bc143ee08ddf"}, "__new_primary_file_jclass.unique.cons|jclass.0.11.ave__": {"src": "hda", "id": "dd278f0ade637866", "uuid": "1c31c901-a39a-48f0-be29-65d0d7569071"}, "__new_primary_file_jclass.unique.cons|jclass.0.32.all__": {"src": "hda", "id": "90768a1b9728ba37", "uuid": "8b50ad5a-d301-4e58-8a01-77f6580dbe9e"}, "__new_primary_file_jclass.unique.cons|jclass.0.19.ave__": {"src": "hda", "id": "15e4d725538ff507", "uuid": "2dd16816-6d80-4dba-83f5-b379d52adb8e"}, "__new_primary_file_jclass.unique.cons|jclass.0.07.cons__": {"src": "hda", "id": "78a5ef7657ea1833", "uuid": "22407272-1b16-44aa-be16-25e717daf1b7"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > tree.shared(shared=input_dist.dat,subsample=T,calc=jclass,processors=1) \r\u001b[A\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[C\u001b[K)\n\nUsing 1 processors.\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_dist.jclass.unique.ave.tre\ninput_dist.jclass.unique.all.tre\ninput_dist.jclass.unique.cons.tre\ninput_dist.jclass.0.01.ave.tre\ninput_dist.jclass.0.01.all.tre\ninput_dist.jclass.0.01.cons.tre\ninput_dist.jclass.0.02.ave.tre\ninput_dist.jclass.0.02.all.tre\ninput_dist.jclass.0.02.cons.tre\ninput_dist.jclass.0.03.ave.tre\ninput_dist.jclass.0.03.all.tre\ninput_dist.jclass.0.03.cons.tre\ninput_dist.jclass.0.04.ave.tre\ninput_dist.jclass.0.04.all.tre\ninput_dist.jclass.0.04.cons.tre\ninput_dist.jclass.0.05.ave.tre\ninput_dist.jclass.0.05.all.tre\ninput_dist.jclass.0.05.cons.tre\ninput_dist.jclass.0.06.ave.tre\ninput_dist.jclass.0.06.all.tre\ninput_dist.jclass.0.06.cons.tre\ninput_dist.jclass.0.07.ave.tre\ninput_dist.jclass.0.07.all.tre\ninput_dist.jclass.0.07.cons.tre\ninput_dist.jclass.0.08.ave.tre\ninput_dist.jclass.0.08.all.tre\ninput_dist.jclass.0.08.cons.tre\ninput_dist.jclass.0.09.ave.tre\ninput_dist.jclass.0.09.all.tre\ninput_dist.jclass.0.09.cons.tre\ninput_dist.jclass.0.10.ave.tre\ninput_dist.jclass.0.10.all.tre\ninput_dist.jclass.0.10.cons.tre\ninput_dist.jclass.0.11.ave.tre\ninput_dist.jclass.0.11.all.tre\ninput_dist.jclass.0.11.cons.tre\ninput_dist.jclass.0.12.ave.tre\ninput_dist.jclass.0.12.all.tre\ninput_dist.jclass.0.12.cons.tre\ninput_dist.jclass.0.13.ave.tre\ninput_dist.jclass.0.13.all.tre\ninput_dist.jclass.0.13.cons.tre\ninput_dist.jclass.0.14.ave.tre\ninput_dist.jclass.0.14.all.tre\ninput_dist.jclass.0.14.cons.tre\ninput_dist.jclass.0.15.ave.tre\ninput_dist.jclass.0.15.all.tre\ninput_dist.jclass.0.15.cons.tre\ninput_dist.jclass.0.16.ave.tre\ninput_dist.jclass.0.16.all.tre\ninput_dist.jclass.0.16.cons.tre\ninput_dist.jclass.0.17.ave.tre\ninput_dist.jclass.0.17.all.tre\ninput_dist.jclass.0.17.cons.tre\ninput_dist.jclass.0.18.ave.tre\ninput_dist.jclass.0.18.all.tre\ninput_dist.jclass.0.18.cons.tre\ninput_dist.jclass.0.19.ave.tre\ninput_dist.jclass.0.19.all.tre\ninput_dist.jclass.0.19.cons.tre\ninput_dist.jclass.0.20.ave.tre\ninput_dist.jclass.0.20.all.tre\ninput_dist.jclass.0.20.cons.tre\ninput_dist.jclass.0.21.ave.tre\ninput_dist.jclass.0.21.all.tre\ninput_dist.jclass.0.21.cons.tre\ninput_dist.jclass.0.22.ave.tre\ninput_dist.jclass.0.22.all.tre\ninput_dist.jclass.0.22.cons.tre\ninput_dist.jclass.0.23.ave.tre\ninput_dist.jclass.0.23.all.tre\ninput_dist.jclass.0.23.cons.tre\ninput_dist.jclass.0.24.ave.tre\ninput_dist.jclass.0.24.all.tre\ninput_dist.jclass.0.24.cons.tre\ninput_dist.jclass.0.25.ave.tre\ninput_dist.jclass.0.25.all.tre\ninput_dist.jclass.0.25.cons.tre\ninput_dist.jclass.0.26.ave.tre\ninput_dist.jclass.0.26.all.tre\ninput_dist.jclass.0.26.cons.tre\ninput_dist.jclass.0.27.ave.tre\ninput_dist.jclass.0.27.all.tre\ninput_dist.jclass.0.27.cons.tre\ninput_dist.jclass.0.29.ave.tre\ninput_dist.jclass.0.29.all.tre\ninput_dist.jclass.0.29.cons.tre\ninput_dist.jclass.0.32.ave.tre\ninput_dist.jclass.0.32.all.tre\ninput_dist.jclass.0.32.cons.tre\ninput_dist.jclass.0.33.ave.tre\ninput_dist.jclass.0.33.all.tre\ninput_dist.jclass.0.33.cons.tre\ninput_dist.jclass.0.36.ave.tre\ninput_dist.jclass.0.36.all.tre\ninput_dist.jclass.0.36.cons.tre\ninput_dist.jclass.0.38.ave.tre\ninput_dist.jclass.0.38.all.tre\ninput_dist.jclass.0.38.cons.tre\ninput_dist.jclass.0.41.ave.tre\ninput_dist.jclass.0.41.all.tre\ninput_dist.jclass.0.41.cons.tre\ninput_dist.jclass.0.45.ave.tre\ninput_dist.jclass.0.45.all.tre\ninput_dist.jclass.0.45.cons.tre\ninput_dist.jclass.0.55.ave.tre\ninput_dist.jclass.0.55.all.tre\ninput_dist.jclass.0.55.cons.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3457.dat' input_dist.dat &&  echo 'tree.shared( shared=input_dist.dat, subsample=T, calc=jclass, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:42:51.798862", "params": {"input": "{\"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 3457}]}, \"__current_case__\": 2, \"label\": null, \"source\": \"shared\", \"groups\": null, \"subsampling\": {\"iters\": \"\", \"subsample\": \"\", \"use\": \"yes\", \"__current_case__\": 0}}", "calc": "\"jclass\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6867", "id": "1380d0b9d445228e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_tree_shared.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"input|label": ["0.05", "0.22", "0.32"], "input|dist": {"src": "hda", "id": "30d3d99850e82b58"}, "input|source": "shared", "input|groups": ["forest", "pasture"], "calc": ["sharedsobs", "sharedchao", "sharedace", "anderberg", "jclass", "jest", "kulczynski", "kulczynskicody", "kstest", "lennon", "ochiai", "sorclass", "sorest", "whittaker", "hamming", "memchi2", "memchord", "memeuclidean", "mempearson", "braycurtis", "jabund", "morisitahorn", "sorabund", "thetan", "thetayc", "canberra", "gower", "hellinger", "manhattan", "odum", "soergel", "spearman", "speciesprofile", 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{"src": "hda", "id": "d1445ecd5410041e", "uuid": "9159e8ff-0cd1-43ae-9972-d4a1049942a8"}, "__new_primary_file_whittaker.0.32|sharedsobs.0.22__": {"src": "hda", "id": "c9da000ecda07245", "uuid": "30f528df-ae4c-4d66-adb6-498a60e6e525"}, "__new_primary_file_whittaker.0.32|odum.0.22__": {"src": "hda", "id": "d018ac0d94e012e8", "uuid": "7b13e8fd-df14-4be5-a637-f14b98e467b2"}, "__new_primary_file_whittaker.0.32|sorest.0.32__": {"src": "hda", "id": "e746dd872753a042", "uuid": "3533d097-f86e-4f80-bab4-0612e4278c8b"}, "__new_primary_file_whittaker.0.32|memchord.0.32__": {"src": "hda", "id": "735efd674719e24f", "uuid": "5469f970-b958-4b90-9d86-8c9a36f7b790"}, "__new_primary_file_whittaker.0.32|hellinger.0.22__": {"src": "hda", "id": "0a8b6862ab30b456", "uuid": "d4170f76-cc41-4a80-937e-d4ea5bf479a1"}, "__new_primary_file_whittaker.0.32|gower.0.05__": {"src": "hda", "id": "4903012a42643751", "uuid": "e8191da1-6091-473a-8708-ade1fb227c27"}, "__new_primary_file_whittaker.0.32|structchi2.0.22__": {"src": "hda", "id": "4396493fbfdb6ad4", "uuid": "3b7e4011-fdb8-484a-a21e-f908efa2acd5"}, "__new_primary_file_whittaker.0.32|hellinger.0.32__": {"src": "hda", "id": "baadb50d03c0b826", "uuid": "b3c0803f-91a9-44eb-8db5-0baba4aa198a"}, "__new_primary_file_whittaker.0.32|hamming.0.05__": {"src": "hda", "id": "6dd4d5ec7dea33a8", "uuid": "511e6489-e5d0-4de6-bb53-87987add5d12"}, "__new_primary_file_whittaker.0.32|kulczynski.0.05__": {"src": "hda", "id": "cd687c1796d12cc6", "uuid": "d1af4501-b106-4652-8931-fc7694dbb0d8"}, "__new_primary_file_whittaker.0.32|jclass.0.05__": {"src": "hda", "id": "a7a6eb5dd94f4973", "uuid": "943c4406-a903-4000-8924-e8680ca58d6a"}, "__new_primary_file_whittaker.0.32|thetayc.0.05__": {"src": "hda", "id": "cd1051f5597a9f45", "uuid": "cc6a47f8-4f98-4a6a-a8ac-c29b7de64308"}, "__new_primary_file_whittaker.0.32|speciesprofile.0.22__": {"src": "hda", "id": "0b9b6fba2374f3e4", "uuid": "3333c796-64f4-4ac5-8b6d-d559be3ede6c"}, "__new_primary_file_whittaker.0.32|soergel.0.22__": {"src": "hda", "id": "d398ff86b62273ad", "uuid": "07795010-5665-45ad-8658-2b809e99f259"}, "__new_primary_file_whittaker.0.32|memchi2.0.05__": {"src": "hda", "id": "a6cfc510c05ff9d2", "uuid": "a923406d-adac-4875-aa54-92355c3da3ff"}, "__new_primary_file_whittaker.0.32|soergel.0.05__": {"src": "hda", "id": "5668ef31ed2adf25", "uuid": "fb53a96f-159d-4383-a215-1500951f3df8"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > tree.shared(shared=input_dist.dat,groups=forest-pasture,label=0.05-0.22 \r-0.32,calc=sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulc \rzynskicody-kstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memcho \rrd-memeuclidean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetay \rc-canberra-gower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-struct \rchi2-structchord-structeuclidean-structkulczynski-structpearson-sharednseqs-shar \redobserved,processors=1)\n\nUsing 1 processors.\nsharedobserved is not a valid estimator for the tree.shared command and will be disregarded. Valid estimators are anderberg, braycurtis, canberra, gower, hamming, hellinger, jabund, jclass, jest, jsd, kstest, kulczynski, kulczynskicody, lennon, manhattan, memchi2, memchord, memeuclidean, mempearson, morisitahorn, ochiai, odum, rjsd, sharedace, sharedchao, sharednseqs, sharedsobs, soergel, sorabund, sorclass, sorest, spearman, speciesprofile, structchi2, structchord, structeuclidean, structkulczynski, structpearson, thetan, thetayc, whittaker, \n0.05\n0.22\n0.32\n\nOutput File Names: \ninput_dist.sharedsobs.0.05.tre\ninput_dist.sharedchao.0.05.tre\ninput_dist.sharedace.0.05.tre\ninput_dist.anderberg.0.05.tre\ninput_dist.jclass.0.05.tre\ninput_dist.jest.0.05.tre\ninput_dist.kulczynski.0.05.tre\ninput_dist.kulczynskicody.0.05.tre\ninput_dist.kstest.0.05.tre\ninput_dist.lennon.0.05.tre\ninput_dist.ochiai.0.05.tre\ninput_dist.sorclass.0.05.tre\ninput_dist.sorest.0.05.tre\ninput_dist.whittaker.0.05.tre\ninput_dist.hamming.0.05.tre\ninput_dist.memchi2.0.05.tre\ninput_dist.memchord.0.05.tre\ninput_dist.memeuclidean.0.05.tre\ninput_dist.mempearson.0.05.tre\ninput_dist.braycurtis.0.05.tre\ninput_dist.jabund.0.05.tre\ninput_dist.morisitahorn.0.05.tre\ninput_dist.sorabund.0.05.tre\ninput_dist.thetan.0.05.tre\ninput_dist.thetayc.0.05.tre\ninput_dist.canberra.0.05.tre\ninput_dist.gower.0.05.tre\ninput_dist.hellinger.0.05.tre\ninput_dist.manhattan.0.05.tre\ninput_dist.odum.0.05.tre\ninput_dist.soergel.0.05.tre\ninput_dist.spearman.0.05.tre\ninput_dist.speciesprofile.0.05.tre\ninput_dist.structchi2.0.05.tre\ninput_dist.structchord.0.05.tre\ninput_dist.structeuclidean.0.05.tre\ninput_dist.structkulczynski.0.05.tre\ninput_dist.structpearson.0.05.tre\ninput_dist.sharednseqs.0.05.tre\ninput_dist.sharedsobs.0.22.tre\ninput_dist.sharedchao.0.22.tre\ninput_dist.sharedace.0.22.tre\ninput_dist.anderberg.0.22.tre\ninput_dist.jclass.0.22.tre\ninput_dist.jest.0.22.tre\ninput_dist.kulczynski.0.22.tre\ninput_dist.kulczynskicody.0.22.tre\ninput_dist.kstest.0.22.tre\ninput_dist.lennon.0.22.tre\ninput_dist.ochiai.0.22.tre\ninput_dist.sorclass.0.22.tre\ninput_dist.sorest.0.22.tre\ninput_dist.whittaker.0.22.tre\ninput_dist.hamming.0.22.tre\ninput_dist.memchi2.0.22.tre\ninput_dist.memchord.0.22.tre\ninput_dist.memeuclidean.0.22.tre\ninput_dist.mempearson.0.22.tre\ninput_dist.braycurtis.0.22.tre\ninput_dist.jabund.0.22.tre\ninput_dist.morisitahorn.0.22.tre\ninput_dist.sorabund.0.22.tre\ninput_dist.thetan.0.22.tre\ninput_dist.thetayc.0.22.tre\ninput_dist.canberra.0.22.tre\ninput_dist.gower.0.22.tre\ninput_dist.hellinger.0.22.tre\ninput_dist.manhattan.0.22.tre\ninput_dist.odum.0.22.tre\ninput_dist.soergel.0.22.tre\ninput_dist.spearman.0.22.tre\ninput_dist.speciesprofile.0.22.tre\ninput_dist.structchi2.0.22.tre\ninput_dist.structchord.0.22.tre\ninput_dist.structeuclidean.0.22.tre\ninput_dist.structkulczynski.0.22.tre\ninput_dist.structpearson.0.22.tre\ninput_dist.sharednseqs.0.22.tre\ninput_dist.sharedsobs.0.32.tre\ninput_dist.sharedchao.0.32.tre\ninput_dist.sharedace.0.32.tre\ninput_dist.anderberg.0.32.tre\ninput_dist.jclass.0.32.tre\ninput_dist.jest.0.32.tre\ninput_dist.kulczynski.0.32.tre\ninput_dist.kulczynskicody.0.32.tre\ninput_dist.kstest.0.32.tre\ninput_dist.lennon.0.32.tre\ninput_dist.ochiai.0.32.tre\ninput_dist.sorclass.0.32.tre\ninput_dist.sorest.0.32.tre\ninput_dist.whittaker.0.32.tre\ninput_dist.hamming.0.32.tre\ninput_dist.memchi2.0.32.tre\ninput_dist.memchord.0.32.tre\ninput_dist.memeuclidean.0.32.tre\ninput_dist.mempearson.0.32.tre\ninput_dist.braycurtis.0.32.tre\ninput_dist.jabund.0.32.tre\ninput_dist.morisitahorn.0.32.tre\ninput_dist.sorabund.0.32.tre\ninput_dist.thetan.0.32.tre\ninput_dist.thetayc.0.32.tre\ninput_dist.canberra.0.32.tre\ninput_dist.gower.0.32.tre\ninput_dist.hellinger.0.32.tre\ninput_dist.manhattan.0.32.tre\ninput_dist.odum.0.32.tre\ninput_dist.soergel.0.32.tre\ninput_dist.spearman.0.32.tre\ninput_dist.speciesprofile.0.32.tre\ninput_dist.structchi2.0.32.tre\ninput_dist.structchord.0.32.tre\ninput_dist.structeuclidean.0.32.tre\ninput_dist.structkulczynski.0.32.tre\ninput_dist.structpearson.0.32.tre\ninput_dist.sharednseqs.0.32.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3567.dat' input_dist.dat &&  echo 'tree.shared( shared=input_dist.dat, groups=forest-pasture, label=0.05-0.22-0.32, calc=sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-kstest-lennon-ochiai-sorclass-sorest-whittaker-hamming-memchi2-memchord-memeuclidean-mempearson-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc-canberra-gower-hellinger-manhattan-odum-soergel-spearman-speciesprofile-structchi2-structchord-structeuclidean-structkulczynski-structpearson-sharednseqs-sharedobserved, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:43:20.325320", "params": {"input": "{\"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 3567}]}, \"__current_case__\": 2, \"label\": [\"0.05\", \"0.22\", \"0.32\"], \"source\": \"shared\", \"groups\": [\"forest\", \"pasture\"], \"subsampling\": {\"use\": \"no\", \"__current_case__\": 1}}", "calc": "[\"sharedsobs\", \"sharedchao\", \"sharedace\", \"anderberg\", \"jclass\", \"jest\", \"kulczynski\", \"kulczynskicody\", \"kstest\", \"lennon\", \"ochiai\", \"sorclass\", \"sorest\", \"whittaker\", \"hamming\", \"memchi2\", \"memchord\", \"memeuclidean\", \"mempearson\", \"braycurtis\", \"jabund\", \"morisitahorn\", \"sorabund\", \"thetan\", \"thetayc\", \"canberra\", \"gower\", \"hellinger\", \"manhattan\", \"odum\", \"soergel\", \"spearman\", \"speciesprofile\", \"structchi2\", \"structchord\", \"structeuclidean\", \"structkulczynski\", \"structpearson\", \"sharednseqs\", \"sharedobserved\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "6951", "id": "0127e3e8a6471eea", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_tree_shared.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input|dist": {"src": "hda", "id": "961a47c559285244"}, "input|name": {"src": "hda", "id": "e579f508f7c68ef6"}, "input|source": "column"}, "job": {"inputs": {"dist": {"src": "hda", "id": "961a47c559285244", "uuid": "8963264e-8c2d-4832-9118-cc2c994c738d"}, "name": {"src": "hda", "id": "e579f508f7c68ef6", "uuid": "f87a42d3-ec48-433f-a653-b4dba9c5f380"}}, "update_time": "2018-02-08T18:43:56.010151", "tool_id": "mothur_tree_shared", "outputs": {"logfile": {"src": "hda", "id": "b96b0bc03c50c213", "uuid": "589355b7-6228-416e-b93d-65ca3f1de74b"}, "tre": {"src": "hda", "id": "1e52af9f521721f4", "uuid": "1e557f11-db81-450e-b091-beb0cf5e8852"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > tree.shared(column=input_dist.dat,name=input_name.dat,calc=jclass-theta \ryc,processors=1)\n\nUsing 1 processors.\n********************#****#****#****#****#****#****#****#****#****#****#\nReading matrix:     ||||||||||||||||||||||||||||||||||||||||||||||||||||\n***********************************************************************\nTree complete. \n\nOutput File Names: \ninput_dist.tre\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3686.dat' input_dist.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3687.dat' input_name.dat &&  echo 'tree.shared( column=input_dist.dat, name=input_name.dat, calc=jclass-thetayc, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:43:52.868228", "params": {"input": "{\"source\": \"column\", \"dist\": {\"values\": [{\"src\": \"hda\", \"id\": 3686}]}, \"name\": {\"values\": [{\"src\": \"hda\", \"id\": 3687}]}, \"__current_case__\": 0}", "calc": "[\"jclass\", \"thetayc\"]", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7076", "id": "d2877f6f2610c2e2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_tree_shared.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"flow": {"src": "hda", "id": "113cebc66d7029f4"}}, "job": {"inputs": {"flow": {"src": "hda", "id": "113cebc66d7029f4", "uuid": "32937a76-7eb0-4ba2-bcf4-1501f91e7efa"}}, "update_time": "2018-02-08T18:44:13.674069", "tool_id": "mothur_trim_flows", "outputs": {"flow_files": {"src": "hda", "id": "656ec4006d660f1e", "uuid": "eb3a4ea6-f598-49c0-bf7d-cc8aa974ac37"}, "logfile": {"src": "hda", "id": "0586ab56d27d9ba2", "uuid": "1fa27a7f-c65a-4225-b91f-1713116e6299"}, "scrap_flow": {"src": "hda", "id": "ea6e776dce59738c", "uuid": "6b64a2db-fc47-4543-8e5a-a8a6129bfeb2"}, "trim_flow": {"src": "hda", "id": "2d34558476a1163b", "uuid": "82fba6fd-ea8d-404e-b6b2-af259e0287dc"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.flows(flow=flow.dat,minflows=450,maxflows=450,order=A,signal=0.5,n \roise=0.7,fasta=false,processors=1)\n\nUsing 1 processors.\n107\n\nOutput File Names: \nflow.trim.flow\nflow.scrap.flow\nflow.flow.files\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3690.dat' flow.dat &&  echo 'trim.flows( flow=flow.dat, minflows=450, maxflows=450, order=A, signal=0.5, noise=0.7, fasta=false, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log  && mv flow.trim.flow flow.trim && mv flow.scrap.flow flow.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:44:10.318502", "params": {"maxflows": "\"450\"", "noise": "\"0.7\"", "oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "signal": "\"0.5\"", "maxhomop": "\"\"", "dbkey": "\"hg17\"", "minflows": "\"450\"", "fasta": "\"false\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "order": "\"A\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7167", "id": "8cd4beb5cf8a2f93", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_flows.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"oligo|oligos": {"src": "hda", "id": "7435327024c6ed38"}, "oligo|add": "yes", "flow": {"src": "hda", "id": "52fb102da68a2516"}, "order": "I", "oligo|pdiffs": "10", "fasta": true, "oligo|bdiffs": "10"}, "job": {"inputs": {"oligos": {"src": "hda", "id": "7435327024c6ed38", "uuid": "b3794253-1136-4bc9-b98d-f61f8a8f4e68"}, "flow": {"src": "hda", "id": "52fb102da68a2516", "uuid": "f0a94d84-d7b8-463c-b0d4-1611c0a29b56"}}, "update_time": "2018-02-08T18:44:45.030422", "tool_id": "mothur_trim_flows", "outputs": {"flow_fasta": {"src": "hda", "id": "1702773de504f46c", "uuid": "4723a1d9-19fe-468b-8190-f08f237f591b"}, "__new_primary_file_F003D142|F003D142__": {"src": "hda", "id": "796a3be2ad26f064", "uuid": "49605ed7-4690-4303-9aee-95d244e32c93"}, "flow_files": {"src": "hda", "id": "ad3afa20e990c280", "uuid": "9180f164-b852-41fc-91c9-fbf5ca513c65"}, "scrap_flow": {"src": "hda", "id": "f30cdc880e9c60f1", "uuid": "7674ae26-298a-4877-afed-884feb505159"}, "__new_primary_file_F003D142|F003D006__": {"src": "hda", "id": "d5d52d49034f5895", "uuid": "fabe0c37-7373-4c45-91cd-9a0761242e9c"}, "logfile": {"src": "hda", "id": "25d2b0eb25240170", "uuid": "ada424ee-49fc-442d-9250-9544ffac7042"}, "trim_flow": {"src": "hda", "id": "d1dd3aa4c719e98f", "uuid": "e8f92f6e-4297-48b2-a305-ec469967806b"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.flows(flow=flow.dat,minflows=450,maxflows=450,order=I,signal=0.5,n \roise=0.7,oligos=oligo.oligos.dat,bdiffs=10,pdiffs=10,tdiffs=0,ldiffs=0,sdiffs=0, \rfasta=true,processors=1)\n\nUsing 1 processors.\n2\n\nOutput File Names: \nflow.flow.fasta\nflow.trim.flow\nflow.scrap.flow\nflow.F003D142.flow\nflow.F003D006.flow\nflow.flow.files\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3695.dat' flow.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3696.dat' oligo.oligos.dat &&  echo 'trim.flows( flow=flow.dat, minflows=450, maxflows=450, order=I, signal=0.5, noise=0.7, oligos=oligo.oligos.dat, bdiffs=10, pdiffs=10, tdiffs=0, ldiffs=0, sdiffs=0, fasta=true, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log  && mv flow.trim.flow flow.trim && mv flow.scrap.flow flow.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:44:41.443491", "params": {"maxflows": "\"450\"", "noise": "\"0.7\"", "oligo": "{\"bdiffs\": \"10\", \"sdiffs\": \"0\", \"ldiffs\": \"0\", \"pdiffs\": \"10\", \"tdiffs\": \"0\", \"add\": \"yes\", \"__current_case__\": 1, \"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 3696}]}}", "signal": "\"0.5\"", "maxhomop": "\"\"", "dbkey": "\"hg17\"", "minflows": "\"450\"", "fasta": "\"true\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "order": "\"I\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7283", "id": "e400af07ae3fa77f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_flows.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "a4a75edff1315423"}, "maxhomop": "4", "names": {"src": "hda", "id": "a19ac8ddc9ec0357"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "a4a75edff1315423", "uuid": "ca78d74b-119e-4138-8c09-5663b94e6bc0"}, "names": {"src": "hda", "id": "a19ac8ddc9ec0357", "uuid": "45c1b563-5ca5-4cf5-802c-c4387f6c28f8"}}, "update_time": "2018-02-08T18:45:30.049751", "tool_id": "mothur_trim_seqs", "outputs": {"trim_fasta": {"src": "hda", "id": "086eda3627b4c383", "uuid": "263d8389-3ec0-45e9-ab3d-6d8a8254cbf5"}, "logfile": {"src": "hda", "id": "4de4e57b6b68d2e8", "uuid": "d9665fcc-9bf4-475a-a4ba-d22174ec9158"}, "trim_names": {"src": "hda", "id": "9590c041f0c58cb5", "uuid": "a15a909d-8f7f-4af5-b173-bcfa30cd0d35"}, "scrap_names": {"src": "hda", "id": "0c5e32c449987b70", "uuid": "f132f816-1a4e-43df-b749-4b6331cb38bf"}, "scrap_fasta": {"src": "hda", "id": "c7132f326e1735c5", "uuid": "083cb5a8-083b-4990-9ecd-f9ad635bc74e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.seqs(fasta=fasta.dat,minlength=0,maxlength=0,maxambig=-1,maxhomop= \r4,keepfirst=0,removelast=0,flip=false,name=names.dat,logtransform=false,checkori \rent=false,processors=1)\n\nUsing 1 processors.\n98\n\n\nOutput File Names: \nfasta.trim.fasta\nfasta.scrap.fasta\nnames.trim.names\nnames.scrap.names\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3704.dat' fasta.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3705.dat' names.dat && ln -s 'None' count.dat &&  echo 'trim.seqs( fasta=fasta.dat, minlength=0, maxlength=0, maxambig=-1, maxhomop=4, keepfirst=0, removelast=0, flip=false, name=names.dat, logtransform=false, checkorient=false, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log  && mv fasta.trim.fasta fasta.trim && mv fasta.scrap.fasta fasta.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:45:26.324404", "params": {"count": "null", "oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "logtransform": "\"false\"", "checkorient": "\"false\"", "minlength": "\"0\"", "maxhomop": "\"4\"", "flip": "\"false\"", "dbkey": "\"hg17\"", "qual": "{\"add2\": \"no\", \"__current_case__\": 0}", "removelast": "\"0\"", "maxlength": "\"0\"", "maxambig": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "keepfirst": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7398", "id": "d9eeaf6b2b0ea17f", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"count": {"src": "hda", "id": "643ecb59a2c3ee18"}, "fasta": {"src": "hda", "id": "411acc63c278eae0"}, "maxhomop": "4"}, "job": {"inputs": {"count": {"src": "hda", "id": "643ecb59a2c3ee18", "uuid": "c3b13bbf-04f4-43f2-87c3-258a8c2718cf"}, "fasta": {"src": "hda", "id": "411acc63c278eae0", "uuid": "3ac2bbb5-576b-4119-aa0e-b61708b757f4"}}, "update_time": "2018-02-08T18:46:09.845777", "tool_id": "mothur_trim_seqs", "outputs": {"trim_fasta": {"src": "hda", "id": "d18b75b0ada0b975", "uuid": "46585795-839f-49f6-9413-87cf07bc4dd8"}, "trim_count": {"src": "hda", "id": "b89907572eef89bb", "uuid": "6a33eeca-8a62-421f-9259-f5c9bb6d75cc"}, "logfile": {"src": "hda", "id": "4a2d02ae29134135", "uuid": "d82b14b6-7d65-4ed0-b8c7-43cab53059bc"}, "scrap_count": {"src": "hda", "id": "0eb01516e0bf5413", "uuid": "1f5a0f89-e35a-4281-9785-c973be1cd403"}, "scrap_fasta": {"src": "hda", "id": "0a20b5e39a223282", "uuid": "9fb65e6d-7f2a-47bb-9c71-a66ebbcc10dd"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.seqs(fasta=fasta.dat,minlength=0,maxlength=0,maxambig=-1,maxhomop= \r4,keepfirst=0,removelast=0,flip=false,logtransform=false,checkorient=false,count \r=count.dat,processors=1)\n\nUsing 1 processors.\n98\n\n\nOutput File Names: \nfasta.trim.fasta\nfasta.scrap.fasta\ncount.trim.count_table\ncount.scrap.count_table\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3711.dat' fasta.dat && ln -s 'None' names.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3712.dat' count.dat &&  echo 'trim.seqs( fasta=fasta.dat, minlength=0, maxlength=0, maxambig=-1, maxhomop=4, keepfirst=0, removelast=0, flip=false, logtransform=false, checkorient=false, count=count.dat, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log  && mv fasta.trim.fasta fasta.trim && mv fasta.scrap.fasta fasta.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:46:05.717799", "params": {"oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "logtransform": "\"false\"", "checkorient": "\"false\"", "minlength": "\"0\"", "maxhomop": "\"4\"", "flip": "\"false\"", "dbkey": "\"hg17\"", "qual": "{\"add2\": \"no\", \"__current_case__\": 0}", "removelast": "\"0\"", "names": "null", "maxlength": "\"0\"", "maxambig": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "keepfirst": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7519", "id": "92afd254baae3cac", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"oligo|pdiffs": "100", "oligo|add": "yes", "fasta": {"src": "hda", "id": "e3535752753237cc"}, "oligo|oligos": {"src": "hda", "id": "449b1393f148b461"}, "oligo|bdiffs": "100"}, "job": {"inputs": {"oligos": {"src": "hda", "id": "449b1393f148b461", "uuid": "d3ecfbe3-82d7-4653-91b3-0dc533243380"}, "fasta": {"src": "hda", "id": "e3535752753237cc", "uuid": "038e784b-9ef9-41ca-be9c-3cd1ca3b8d1e"}}, "update_time": "2018-02-08T18:46:49.872573", "tool_id": "mothur_trim_seqs", "outputs": {"trim_fasta": {"src": "hda", "id": "58247062b75fcc28", "uuid": "7ed9fab5-b057-4f16-98d9-fcc76b26eaf7"}, "groups_file": {"src": "hda", "id": "51245ff49e713d95", "uuid": "f1155b05-066a-42b0-b884-3f16249b6e09"}, "logfile": {"src": "hda", "id": "72a0b075a3958e20", "uuid": "9c442237-3f36-4b3c-88fa-befa7ad3ccc2"}, "scrap_fasta": {"src": "hda", "id": "3aa93502f78ca78e", "uuid": "cc655219-5ebe-4c48-8b2a-5a3d198e6869"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.seqs(fasta=fasta.dat,minlength=0,maxlength=0,maxambig=-1,maxhomop= \r0,keepfirst=0,removelast=0,oligos=oligo.oligos.dat,bdiffs=100,pdiffs=100,tdiffs= \r0,ldiffs=0,sdiffs=0,keepforward=false,allfiles=false,flip=false,logtransform=fal \rse,checkorient=false,processors=1)\n\nUsing 1 processors.\n98\n\nGroup count: \nF003D000\t32\nF003D006\t1\nF003D008\t3\nF003D142\t7\nF003D144\t8\nF003D146\t4\nF003D148\t33\nF003D150\t1\nMOCK.GQY1XT001\t2\nTotal of all groups is 91\n\nOutput File Names: \nfasta.trim.fasta\nfasta.scrap.fasta\nfasta.groups\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3718.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3719.dat' oligo.oligos.dat &&  echo 'trim.seqs( fasta=fasta.dat, minlength=0, maxlength=0, maxambig=-1, maxhomop=0, keepfirst=0, removelast=0, oligos=oligo.oligos.dat, bdiffs=100, pdiffs=100, tdiffs=0, ldiffs=0, sdiffs=0, keepforward=false, allfiles=false, flip=false, logtransform=false, checkorient=false, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log  && mv fasta.trim.fasta fasta.trim && mv fasta.scrap.fasta fasta.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:46:46.434270", "params": {"count": "null", "oligo": "{\"bdiffs\": \"100\", \"sdiffs\": \"0\", \"allfiles\": \"false\", \"ldiffs\": \"0\", \"pdiffs\": \"100\", \"tdiffs\": \"0\", \"keepforward\": \"false\", \"add\": \"yes\", \"__current_case__\": 1, \"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 3719}]}}", "logtransform": "\"false\"", "checkorient": "\"false\"", "minlength": "\"0\"", "maxhomop": "\"0\"", "flip": "\"false\"", "dbkey": "\"hg17\"", "qual": "{\"add2\": \"no\", \"__current_case__\": 0}", "removelast": "\"0\"", "names": "null", "maxlength": "\"0\"", "maxambig": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "keepfirst": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7643", "id": "ab005d4cdb71cef2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"oligo|oligos": {"src": "hda", "id": "4fa21a2ab98d6a11"}, "oligo|add": "yes", "oligo|allfiles": true, "oligo|pdiffs": "100", "fasta": {"src": "hda", "id": "8f862e98c671efbc"}, "oligo|bdiffs": "100"}, "job": {"inputs": {"oligos": {"src": "hda", "id": "4fa21a2ab98d6a11", "uuid": "4f8eff6d-55e5-415a-bc0d-c2d29719aeba"}, "fasta": {"src": "hda", "id": "8f862e98c671efbc", "uuid": "4db73f9a-c8d2-4412-a03a-1e97a9d88de9"}}, "update_time": "2018-02-08T18:47:24.871409", "tool_id": "mothur_trim_seqs", "outputs": {"__new_primary_file_MOCK.GQY1XT001|F003D142__": {"src": "hda", "id": "e2a4c2b0e0ee29b7", "uuid": "a6fdc088-e73a-40f8-bf55-e4e6b05e6df6"}, "__new_primary_file_MOCK.GQY1XT001|F003D008__": {"src": "hda", "id": "d3e37e974b33cd78", "uuid": "326975c6-ec31-4566-bdf9-992bf271f3fb"}, "trim_fasta": {"src": "hda", "id": "d3b573d52d73e766", "uuid": "aac454ae-8526-4fd9-814b-a1fcd172b940"}, "__new_primary_file_MOCK.GQY1XT001|F003D006__": {"src": "hda", "id": "bc7fa00e824e36c4", "uuid": "60d14df6-432d-4d0f-8313-f0ae7c23a9fe"}, "__new_primary_file_MOCK.GQY1XT001|F003D144__": {"src": "hda", "id": "0476296d69f55ec7", "uuid": "800f3e5c-b564-4b05-8b4e-10393cf64eb5"}, "groups_file": {"src": "hda", "id": "521e581659a1db8a", "uuid": "7d8467df-a299-4ab5-981c-809d2c955ab8"}, "__new_primary_file_MOCK.GQY1XT001|MOCK.GQY1XT001__": {"src": "hda", "id": "6bedfbc6c2ea7489", "uuid": "e0de8a75-b145-4e48-8be9-bd44ba70fa91"}, "scrap_fasta": {"src": "hda", "id": "f5a3628d40cdc020", "uuid": "2daaa7dd-b657-4bab-9daf-774b27ed03d1"}, "__new_primary_file_MOCK.GQY1XT001|F003D000__": {"src": "hda", "id": "e55fe44fe41229c1", "uuid": "e20e9144-4c6b-4fc7-88ab-0c7752e46b6c"}, "__new_primary_file_MOCK.GQY1XT001|F003D150__": {"src": "hda", "id": "ea11db34dbe66961", "uuid": "0973157d-fa0f-4060-b1d7-9fbbcc01ee45"}, "logfile": {"src": "hda", "id": "227335580a9b176b", "uuid": "da08afb2-6cc3-4c9d-a89c-ac1d2243af70"}, "__new_primary_file_MOCK.GQY1XT001|F003D146__": {"src": "hda", "id": "2e2129d42462228f", "uuid": "617ed727-566c-4679-83a7-3c1e15e38d8f"}, "__new_primary_file_MOCK.GQY1XT001|F003D148__": {"src": "hda", "id": "b2e57fd9cecc5aab", "uuid": "5ebc12ad-7f12-47b2-871c-d84ee6e05504"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.seqs(fasta=fasta.dat,minlength=0,maxlength=0,maxambig=-1,maxhomop= \r0,keepfirst=0,removelast=0,oligos=oligo.oligos.dat,bdiffs=100,pdiffs=100,tdiffs= \r0,ldiffs=0,sdiffs=0,keepforward=false,allfiles=true,flip=false,logtransform=fals \re,checkorient=false,processors=1)\n\nUsing 1 processors.\n98\n\nGroup count: \nF003D000\t32\nF003D006\t1\nF003D008\t3\nF003D142\t7\nF003D144\t8\nF003D146\t4\nF003D148\t33\nF003D150\t1\nMOCK.GQY1XT001\t2\nTotal of all groups is 91\n\nOutput File Names: \nfasta.trim.fasta\nfasta.scrap.fasta\nfasta.MOCK.GQY1XT001.fasta\nfasta.F003D144.fasta\nfasta.F003D000.fasta\nfasta.F003D148.fasta\nfasta.F003D142.fasta\nfasta.F003D146.fasta\nfasta.F003D150.fasta\nfasta.F003D008.fasta\nfasta.F003D006.fasta\nfasta.groups\nfasta.F003D000.groups\nfasta.F003D006.groups\nfasta.F003D008.groups\nfasta.F003D142.groups\nfasta.F003D144.groups\nfasta.F003D146.groups\nfasta.F003D148.groups\nfasta.F003D150.groups\nfasta.MOCK.GQY1XT001.groups\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3724.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3725.dat' oligo.oligos.dat &&  echo 'trim.seqs( fasta=fasta.dat, minlength=0, maxlength=0, maxambig=-1, maxhomop=0, keepfirst=0, removelast=0, oligos=oligo.oligos.dat, bdiffs=100, pdiffs=100, tdiffs=0, ldiffs=0, sdiffs=0, keepforward=false, allfiles=true, flip=false, logtransform=false, checkorient=false, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log  && mv fasta.trim.fasta fasta.trim && mv fasta.scrap.fasta fasta.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:47:20.369148", "params": {"count": "null", "oligo": "{\"bdiffs\": \"100\", \"sdiffs\": \"0\", \"allfiles\": \"true\", \"ldiffs\": \"0\", \"pdiffs\": \"100\", \"tdiffs\": \"0\", \"keepforward\": \"false\", \"add\": \"yes\", \"__current_case__\": 1, \"oligos\": {\"values\": [{\"src\": \"hda\", \"id\": 3725}]}}", "logtransform": "\"false\"", "checkorient": "\"false\"", "minlength": "\"0\"", "maxhomop": "\"0\"", "flip": "\"false\"", "dbkey": "\"hg17\"", "qual": "{\"add2\": \"no\", \"__current_case__\": 0}", "removelast": "\"0\"", "names": "null", "maxlength": "\"0\"", "maxambig": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "keepfirst": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7764", "id": "093ebc9d412c603b", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_seqs.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"qual|qfile": {"src": "hda", "id": "7934594c89e91a33"}, "fasta": {"src": "hda", "id": "fc95eb28ec7fe06a"}, "maxhomop": "4", "qual|add2": "yes"}, "job": {"inputs": {"fasta": {"src": "hda", "id": "fc95eb28ec7fe06a", "uuid": "0211fde4-c693-40d3-9b5b-5912e37414d7"}, "qfile": {"src": "hda", "id": "7934594c89e91a33", "uuid": "8b3f866a-c0fe-4a8b-bfe7-af9154ac6314"}}, "update_time": "2018-02-08T18:48:03.759616", "tool_id": "mothur_trim_seqs", "outputs": {"trim_fasta": {"src": "hda", "id": "815697d3d9eb26cb", "uuid": "caf56444-922f-4eee-bc2a-ff2fa5851073"}, "logfile": {"src": "hda", "id": "44f0746e84939f78", "uuid": "34d43e05-0980-4046-97ba-0ed5252d8e66"}, "scrap_qual": {"src": "hda", "id": "7ddeb7c19c1d7c5a", "uuid": "da3e9833-2cb7-4b2d-a02b-2c6b2cec0918"}, "scrap_fasta": {"src": "hda", "id": "454e9e805ca4077a", "uuid": "d7dd29ef-d688-476f-b7a7-05bf9d8715e8"}, "trim_qual": {"src": "hda", "id": "676dc9710b90c439", "uuid": "7ca5b932-3be9-4b70-8274-32b64dc5e60e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > trim.seqs(fasta=fasta.dat,minlength=0,maxlength=0,maxambig=-1,maxhomop= \r4,keepfirst=0,removelast=0,qfile=qual.qfile.dat,qaverage=0,qthreshold=0,qwindowa \rverage=0,qwindowsize=50,rollaverage=0,qstepsize=1,qtrim=false,flip=false,logtran \rsform=false,checkorient=false,processors=1)\n\nUsing 1 processors.\n10\n\n\nOutput File Names: \nfasta.trim.fasta\nfasta.scrap.fasta\nfasta.trim.qual\nfasta.scrap.qual\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3748.dat' fasta.dat && ln -s 'None' names.dat && ln -s 'None' count.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3749.dat' qual.qfile.dat &&  echo 'trim.seqs( fasta=fasta.dat, minlength=0, maxlength=0, maxambig=-1, maxhomop=4, keepfirst=0, removelast=0, qfile=qual.qfile.dat, qaverage=0, qthreshold=0, qwindowaverage=0, qwindowsize=50, rollaverage=0, qstepsize=1, qtrim=false, flip=false, logtransform=false, checkorient=false, processors='${GALAXY_SLOTS:-8}' )' | sed 's/ //g' | mothur | tee mothur.out.log  && mv fasta.trim.fasta fasta.trim && mv fasta.scrap.fasta fasta.scrap", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:48:00.227292", "params": {"count": "null", "oligo": "{\"add\": \"no\", \"__current_case__\": 0}", "logtransform": "\"false\"", "checkorient": "\"false\"", "minlength": "\"0\"", "maxhomop": "\"4\"", "flip": "\"false\"", "dbkey": "\"hg17\"", "qual": "{\"qaverage\": \"0\", \"add2\": \"yes\", \"rollaverage\": \"0\", \"qfile\": {\"values\": [{\"src\": \"hda\", \"id\": 3749}]}, \"qwindowaverage\": \"0\", \"qthreshold\": \"0\", \"__current_case__\": 1, \"qstepsize\": \"1\", \"qtrim\": \"false\", \"qwindowsize\": \"50\"}", "removelast": "\"0\"", "names": "null", "maxlength": "\"0\"", "maxambig": "\"-1\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "keepfirst": "\"0\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7890", "id": "ef11ae9dd5e1ab5d", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_trim_seqs.test_tool_000004", "has_data": true}, {"data": {"status": "success", "inputs": {"tree": {"src": "hda", "id": "6df0b8642431f7cc"}}, "job": {"inputs": {"tree": {"src": "hda", "id": "6df0b8642431f7cc", "uuid": "6b1c9231-0e1e-4386-a8c2-c68780fddaad"}}, "update_time": "2018-02-08T18:48:36.539810", "tool_id": "mothur_unifrac_unweighted", "outputs": {"logfile": {"src": "hda", "id": "4b2a9422f173d099", "uuid": "22237f41-b2fc-4fcc-9f91-ad1c58ef660d"}, "dist": {"src": "hda", "id": "8ade91c37a8a22e4", "uuid": "1521df49-9e17-4089-af80-1e8cde0e428c"}, "summary": {"src": "hda", "id": "369c1a55ae4ea50a", "uuid": "f5953986-44ae-4b23-8259-a72c04e04771"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.unweighted(tree=tree.dat,iters=1000,random=false,distance=lt,ro \rot=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tUWScore\t\n1\t\t1\nIt took 0 secs to run unifrac.unweighted.\n\nOutput File Names: \ntree.uwsummary\ntree.dat1.unweighted.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3755.dat' tree.dat && ln -s 'None' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'unifrac.unweighted( tree=tree.dat, iters=1000, random=false, distance=lt, root=false, processors='${GALAXY_SLOTS:-1}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:48:33.297630", "params": {"count": "null", "distance": "\"lt\"", "group": "null", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"false\"", "dbkey": "\"hg17\"", "groups": "null", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "7995", "id": "72b2b39740f9703c", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_unweighted.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"random": true, "tree": {"src": "hda", "id": "a42959d25b93204d"}}, "job": {"inputs": {"tree": {"src": "hda", "id": "a42959d25b93204d", "uuid": "cc159f63-71d4-43f6-bb06-ca3860641095"}}, "update_time": "2018-02-08T18:48:59.691564", "tool_id": "mothur_unifrac_unweighted", "outputs": {"unweighted": {"src": "hda", "id": "1afbdcbd8124b81c", "uuid": "bd550cfe-d7f3-4576-afbc-732ed1cd0ad1"}, "logfile": {"src": "hda", "id": "5882c2146ac78717", "uuid": "4d57d082-d71e-4cea-aced-050026f1cbb0"}, "dist": {"src": "hda", "id": "ebca56f6202f73d0", "uuid": "d80f9213-4452-4e9e-8cc3-89354629bf11"}, "summary": {"src": "hda", "id": "17941f39887c26fe", "uuid": "70d01ba9-c07d-42e9-93d0-36bfe05590eb"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.unweighted(tree=tree.dat,iters=1000,random=true,distance=lt,roo \rt=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tUWScore\tUWSig\n1\t\t1\t1\nIt took 0 secs to run unifrac.unweighted.\n\nOutput File Names: \ntree.uwsummary\ntree.dat1.unweighted\ntree.dat1.unweighted.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3759.dat' tree.dat && ln -s 'None' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'unifrac.unweighted( tree=tree.dat, iters=1000, random=true, distance=lt, root=false, processors='${GALAXY_SLOTS:-1}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:48:55.837836", "params": {"count": "null", "distance": "\"lt\"", "group": "null", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"true\"", "dbkey": "\"hg17\"", "groups": "null", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8087", "id": "957ab5f6bc45f41a", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_unweighted.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "216531b9838bcc19"}, "tree": {"src": "hda", "id": "13cac33be07cea40"}, "groups": ["A", "B"], "distance": "square"}, "job": {"inputs": {"group": {"src": "hda", "id": "216531b9838bcc19", "uuid": "8ec7f52a-4be6-4ffd-b896-9fdc0e76d0d5"}, "tree": {"src": "hda", "id": "13cac33be07cea40", "uuid": "7a20c32c-6646-4271-b2a1-f89e11ae55fa"}}, "update_time": "2018-02-08T18:49:28.670980", "tool_id": "mothur_unifrac_unweighted", "outputs": {"logfile": {"src": "hda", "id": "832ffb62535b10da", "uuid": "17c0f6f4-784c-44e5-8c94-f6f13fe4f737"}, "dist": {"src": "hda", "id": "91be6474cef830ab", "uuid": "95704f3c-80a0-4fbf-83c7-65d4cbabf9bf"}, "summary": {"src": "hda", "id": "28795f877f71134f", "uuid": "83719290-947c-48da-99fc-95049a661051"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.unweighted(tree=tree.dat,group=group.dat,groups=A-B,iters=1000, \rrandom=false,distance=square,root=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tUWScore\t\n1\tA-B\t0.697429\nIt took 0 secs to run unifrac.unweighted.\n\nOutput File Names: \ntree.uwsummary\ntree.dat1.unweighted.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3764.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3765.dat' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'unifrac.unweighted( tree=tree.dat, group=group.dat, groups=A-B, iters=1000, random=false, distance=square, root=false, processors='${GALAXY_SLOTS:-1}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:49:25.419654", "params": {"count": "null", "distance": "\"square\"", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"false\"", "dbkey": "\"hg17\"", "groups": "[\"A\", \"B\"]", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8200", "id": "dd4d919ea4ea0b29", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_unweighted.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"distance": "column", "group": {"src": "hda", "id": "5e10cd539f2a6619"}, "tree": {"src": "hda", "id": "9aac823dc8c01e16"}, "subsampling|subsample": "10", "groups": ["A", "B", "C"], "subsampling|consensus": true, "subsampling|use": "yes"}, "job": {"inputs": {"group": {"src": "hda", "id": "5e10cd539f2a6619", "uuid": "9afe7468-0185-4855-a9d4-68c0b8ebeb85"}, "tree": {"src": "hda", "id": "9aac823dc8c01e16", "uuid": "5b6b7751-6143-41bc-9921-39b157b4c9e2"}}, "update_time": "2018-02-08T18:49:55.348485", "tool_id": "mothur_unifrac_unweighted", "outputs": {"logfile": {"src": "hda", "id": "5c1603539e28a1c0", "uuid": "08ea5982-30fa-4993-8384-32ab676d85a2"}, "dist": {"src": "hda", "id": "fe4fbad99aec603a", "uuid": "662ee7f3-d3d3-47b0-ab8b-0e3bb348a1ec"}, "cons_tree": {"src": "hda", "id": "c0615e4cb678cabf", "uuid": "bf2192d8-30bc-410c-baca-9ca1823a491c"}, "all_tree": {"src": "hda", "id": "727b1362191da7aa", "uuid": "9a7fe375-9d3f-41dc-9620-cd3e0ac5daa9"}, "ave_dist": {"src": "hda", "id": "ac3107c78c55b210", "uuid": "e16d304c-a86d-4ca0-ab05-32078b53e0f2"}, "std_dist": {"src": "hda", "id": "a04ba41073d3fea6", "uuid": "2319c776-e083-4364-9b61-aba0a91cd913"}, "summary": {"src": "hda", "id": "1cc9930f120e2a4c", "uuid": "9077764c-0952-4a37-a295-7dff1491718f"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.unweighted(tree=tree.dat,group=group.dat,groups=A-B-C,iters=100 \r0,subsample=10,consensus=true,distance=column,root=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tUWScore\t\n100\n200\n300\n400\n500\n600\n700\n800\n900\n1000\nIt took 1 secs to run the subsampling.\n1\tA-B\t0.697429\n1\tA-C\t0.745247\n1\tB-C\t0.779964\nIt took 1 secs to run unifrac.unweighted.\n\nOutput File Names: \ntree.uwsummary\ntree.1.unweighted.ave.dist\ntree.1.unweighted.std.dist\ntree.1.unweighted.all.tre\ntree.1.unweighted.cons.tre\ntree.dat1.unweighted.column.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3769.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3770.dat' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'unifrac.unweighted( tree=tree.dat, group=group.dat, groups=A-B-C, iters=1000, subsample=10, consensus=true, distance=column, root=false, processors='${GALAXY_SLOTS:-1}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:49:51.083299", "params": {"count": "null", "distance": "\"column\"", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"false\"", "dbkey": "\"hg17\"", "groups": "[\"A\", \"B\", \"C\"]", "subsampling": "{\"consensus\": \"true\", \"subsample\": \"10\", \"use\": \"yes\", \"__current_case__\": 0}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8325", "id": "025a944d63daedd1", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_unweighted.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "0838a9bd40f5c4ce"}, "tree": {"src": "hda", "id": "b3462b19f4f15b33"}, "groups": ["A", "B", "C"]}, "job": {"inputs": {"group": {"src": "hda", "id": "0838a9bd40f5c4ce", "uuid": "8c75c923-d3db-4d38-9bb8-0bbfc949fa33"}, "tree": {"src": "hda", "id": "b3462b19f4f15b33", "uuid": "b462b4a8-88cf-41dc-bdb9-05a127fd8063"}}, "update_time": "2018-02-08T18:50:45.499239", "tool_id": "mothur_unifrac_weighted", "outputs": {"logfile": {"src": "hda", "id": "3fa7183d0a1b019b", "uuid": "08246390-a6be-4f84-ad75-9fa451c35c8a"}, "dist": {"src": "hda", "id": "79e7be5d12af6385", "uuid": "cfb6f0a5-f72a-4422-a72c-54e43dcbcd92"}, "summary": {"src": "hda", "id": "3a27c90fe001e6a6", "uuid": "002b5114-c0be-4d27-bf98-f2dd5c64f619"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.weighted(tree=tree.dat,group=group.dat,groups=A-B-C,iters=1000, \rrandom=false,distance=lt,root=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tWScore\t\n1\tA-B\t0.420804\n1\tA-C\t0.561036\n1\tB-C\t0.614747\nIt took 0 secs to run unifrac.weighted.\n\nOutput File Names: \ntree.datwsummary\ntree.dat1.weighted.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3778.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3779.dat' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'unifrac.weighted( tree=tree.dat, group=group.dat, groups=A-B-C, iters=1000, random=false, distance=lt, root=false, processors='${GALAXY_SLOTS:-1}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:50:41.538022", "params": {"count": "null", "distance": "\"lt\"", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"false\"", "dbkey": "\"hg17\"", "groups": "[\"A\", \"B\", \"C\"]", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8452", "id": "79a8c1c389391c2e", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_weighted.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "518ff5e2cb49d7bb"}, "random": true, "tree": {"src": "hda", "id": "fd6333f7835dfe44"}, "groups": ["A", "B", "C"]}, "job": {"inputs": {"group": {"src": "hda", "id": "518ff5e2cb49d7bb", "uuid": "c1210880-04ea-42f6-894f-4590ed23d2a4"}, "tree": {"src": "hda", "id": "fd6333f7835dfe44", "uuid": "7adf2d3b-f9f0-496f-a251-f63bb1005228"}}, "update_time": "2018-02-08T18:51:16.087597", "tool_id": "mothur_unifrac_weighted", "outputs": {"logfile": {"src": "hda", "id": "6c3534f8df79d924", "uuid": "dc7c40ce-158b-4448-b303-fe3039aedc6c"}, "dist": {"src": "hda", "id": "63d28ef2435a4446", "uuid": "d696ec13-f4b0-49be-bae0-ae193f12965d"}, "summary": {"src": "hda", "id": "160ab7f4e3f4c4c1", "uuid": "7723ec4a-7e76-4135-9a4e-bad716710dba"}, "weighted": {"src": "hda", "id": "bd78fbbdf8dac536", "uuid": "269c6665-e3c2-45b2-88a9-b6bc101436af"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.weighted(tree=tree.dat,group=group.dat,groups=A-B-C,iters=1000, \rrandom=true,distance=lt,root=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tWScore\tWSig\n1\tA-B\t0.420804\t<0.001\n1\tA-C\t0.561036\t<0.001\n1\tB-C\t0.614747\t<0.001\nIt took 3 secs to run unifrac.weighted.\n\nOutput File Names: \ntree.datwsummary\ntree.dat1.weighted\ntree.dat1.weighted.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3783.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3784.dat' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'unifrac.weighted( tree=tree.dat, group=group.dat, groups=A-B-C, iters=1000, random=true, distance=lt, root=false, processors='${GALAXY_SLOTS:-1}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:51:10.189404", "params": {"count": "null", "distance": "\"lt\"", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"true\"", "dbkey": "\"hg17\"", "groups": "[\"A\", \"B\", \"C\"]", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8562", "id": "9140d1ef204facd8", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_weighted.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"group": {"src": "hda", "id": "22fc2c025e64e76f"}, "tree": {"src": "hda", "id": "31e4d008821c6455"}, "groups": ["A", "B"], "distance": "square"}, "job": {"inputs": {"group": {"src": "hda", "id": "22fc2c025e64e76f", "uuid": "0b953332-ddcc-4b42-9fbd-df180e3a79af"}, "tree": {"src": "hda", "id": "31e4d008821c6455", "uuid": "ccae7e6c-1d7d-42b7-bb86-10ab235256ce"}}, "update_time": "2018-02-08T18:51:47.265203", "tool_id": "mothur_unifrac_weighted", "outputs": {"logfile": {"src": "hda", "id": "584bfbb334e631ee", "uuid": "b8815e25-4a19-41b2-b938-6d6b82239ec8"}, "dist": {"src": "hda", "id": "48f366354bcadc71", "uuid": "5d7c5c74-5472-4d42-b883-1e89e9f05a3a"}, "summary": {"src": "hda", "id": "d6c62cf9da0ecb9f", "uuid": "a001986d-fbef-433c-af54-230fd2fde10e"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.weighted(tree=tree.dat,group=group.dat,groups=A-B,iters=1000,ra \rndom=false,distance=square,root=false,processors=1)\n\nUsing 1 processors.\nTree#\tGroups\tWScore\t\n1\tA-B\t0.420804\nIt took 0 secs to run unifrac.weighted.\n\nOutput File Names: \ntree.datwsummary\ntree.dat1.weighted.phylip.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3789.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3790.dat' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'unifrac.weighted( tree=tree.dat, group=group.dat, groups=A-B, iters=1000, random=false, distance=square, root=false, processors='${GALAXY_SLOTS:-1}' )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:51:44.075183", "params": {"count": "null", "distance": "\"square\"", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"false\"", "dbkey": "\"hg17\"", "groups": "[\"A\", \"B\"]", "subsampling": "{\"use\": \"no\", \"__current_case__\": 1}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8690", "id": "fa032b562e153122", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_weighted.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"distance": "column", "group": {"src": "hda", "id": "794af97c9033590e"}, "tree": {"src": "hda", "id": "a21fe8ee9e63080c"}, "subsampling|subsample": "10", "groups": ["A", "B", "C"], "subsampling|consensus": true, "subsampling|use": "yes"}, "job": {"inputs": {"group": {"src": "hda", "id": "794af97c9033590e", "uuid": "e20175cd-14b3-49b4-bfce-0142810ff7f3"}, "tree": {"src": "hda", "id": "a21fe8ee9e63080c", "uuid": "fc7d7c2f-d877-492e-83b3-f66d55da81e0"}}, "update_time": "2018-02-08T18:52:14.538020", "tool_id": "mothur_unifrac_weighted", "outputs": {"logfile": {"src": "hda", "id": "5ba55d6a72b87324", "uuid": "f365a4ac-3eab-4c3f-8f34-05411cea8df0"}, "dist": {"src": "hda", "id": "60b877016be95026", "uuid": "f7db84a3-f1f3-4995-a595-b9b554cb6987"}, "cons_tree": {"src": "hda", "id": "c2e52dbcfe49c36d", "uuid": "9f1ef3be-aaff-4eb4-aa98-a5a58105c962"}, "all_tree": {"src": "hda", "id": "707ccea25fc9dd71", "uuid": "f59c4ad1-d5b9-4170-a839-eeb5cbf1e7bf"}, "ave_dist": {"src": "hda", "id": "24b1957315221820", "uuid": "384c63b7-3e46-4cfb-9d54-32a87a8cc979"}, "std_dist": {"src": "hda", "id": "e1f6007d0d1998af", "uuid": "55fe1249-c6a4-4367-b8b8-d0c128cb6473"}, "summary": {"src": "hda", "id": "f478481875067414", "uuid": "f03af451-dab2-4f4d-b556-0339cc0cce02"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unifrac.weighted(tree=tree.dat,group=group.dat,groups=A-B-C,iters=1000, \rsubsample=10,consensus=true,distance=column,root=false,processors=1)\n\nUsing 1 processors.\n100\n200\n300\n400\n500\n600\n700\n800\n900\n1000\nTree#\tGroups\tWScore\t\n1\tA-B\t0.420804\n1\tA-C\t0.561036\n1\tB-C\t0.614747\nIt took 1 secs to run unifrac.weighted.\n\nOutput File Names: \ntree.datwsummary\ntree.dat1.weighted.ave.dist\ntree.dat1.weighted.std.dist\ntree.1.weighted.all.tre\ntree.1.weighted.cons.tre\ntree.dat1.weighted.column.dist\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3794.dat' tree.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3795.dat' group.dat && ln -s 'None' name.dat && ln -s 'None' count.dat &&  echo 'unifrac.weighted( tree=tree.dat, group=group.dat, groups=A-B-C, iters=1000, subsample=10, consensus=true, distance=column, root=false, processors='${GALAXY_SLOTS:-1}' )' | sed 's/ //g' | mothur | tee mothur.out.log  && mv tree.*.ave.dist tree.ave && mv tree.*.std.dist tree.std", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:52:09.934321", "params": {"count": "null", "distance": "\"column\"", "name": "null", "iters": "\"1000\"", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "random": "\"false\"", "dbkey": "\"hg17\"", "groups": "[\"A\", \"B\", \"C\"]", "subsampling": "{\"consensus\": \"true\", \"subsample\": \"10\", \"use\": \"yes\", \"__current_case__\": 0}", "root": "\"false\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8802", "id": "b1d26ebda0776d51", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unifrac_weighted.test_tool_000003", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "f8823dc7d466d97b"}, "names": {"src": "hda", "id": "8187faee9c922310"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "f8823dc7d466d97b", "uuid": "eb69bb90-2c63-414e-9416-14bac878965b"}, "names": {"src": "hda", "id": "8187faee9c922310", "uuid": "bc005bee-5b71-43d0-9208-591b7c0ccd59"}}, "update_time": "2018-02-08T18:53:02.690147", "tool_id": "mothur_unique_seqs", "outputs": {"out_names": {"src": "hda", "id": "8b0f9f257ede5df4", "uuid": "41b0e472-5881-44be-8df3-b79fe480143f"}, "logfile": {"src": "hda", "id": "f3df144761c5b956", "uuid": "5dc05b2e-6f8a-48b7-82ed-e1ff821dba29"}, "out_fasta": {"src": "hda", "id": "66d3fd607ddc158a", "uuid": "53038c6e-0d47-4faa-aa0d-e1db2f95bfc9"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unique.seqs(name=names.dat,fasta=fasta.dat)\n98\t96\n\nOutput File Names: \nfasta.names\nfasta.unique.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3804.dat' names.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3803.dat' fasta.dat &&  echo 'unique.seqs( name=names.dat, fasta=fasta.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:52:59.577595", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "8930", "id": "c239c296c8b002ba", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unique_seqs.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "8aaa031deda3761e"}, "names": {"src": "hda", "id": "864bc422cb6c6663"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "8aaa031deda3761e", "uuid": "cbb5a981-dd46-4e6d-a26b-0f7397e76300"}, "names": {"src": "hda", "id": "864bc422cb6c6663", "uuid": "ca478712-7077-485d-bbf7-d6349244011d"}}, "update_time": "2018-02-08T18:53:28.461742", "tool_id": "mothur_unique_seqs", "outputs": {"out_count": {"src": "hda", "id": "b1b0e3e670e9fef5", "uuid": "b6579f3e-d17c-4ae3-9909-afe68c12e00d"}, "logfile": {"src": "hda", "id": "5cdc51911a37e673", "uuid": "08e8438b-a641-43e4-83f2-47bcb535c92e"}, "out_fasta": {"src": "hda", "id": "5fab573ff4009995", "uuid": "838a2f8a-9284-4d3e-a768-0a69cb33a7d4"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unique.seqs(count=names.dat,fasta=fasta.dat)\n96\t96\n\nOutput File Names: \nfasta.count_table\nfasta.unique.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3809.dat' names.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3808.dat' fasta.dat &&  echo 'unique.seqs( count=names.dat, fasta=fasta.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:53:25.211028", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9040", "id": "5498b8b462f50992", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unique_seqs.test_tool_000001", "has_data": true}, {"data": {"status": "success", "inputs": {"fasta": {"src": "hda", "id": "7b00e7fa90e73a2c"}}, "job": {"inputs": {"fasta": {"src": "hda", "id": "7b00e7fa90e73a2c", "uuid": "8dbab685-56c7-4b8f-b547-9f2f9bfb7cf2"}}, "update_time": "2018-02-08T18:53:51.166544", "tool_id": "mothur_unique_seqs", "outputs": {"out_names": {"src": "hda", "id": "ddd777d89c6d8995", "uuid": "eb0f6782-ae6b-4df5-9e88-2eaca0da2a0c"}, "logfile": {"src": "hda", "id": "6e4eaae38f2fd10c", "uuid": "efec61f4-381e-4e05-ba55-0d10262d1963"}, "out_fasta": {"src": "hda", "id": "ea5794814dd23e3d", "uuid": "33dadcf5-75a9-4702-8a3a-745d0bf290a5"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > unique.seqs(fasta=fasta.dat)\n98\t96\n\nOutput File Names: \nfasta.names\nfasta.unique.dat\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s 'None' names.dat && ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3813.dat' fasta.dat &&  echo 'unique.seqs( fasta=fasta.dat )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:53:47.926817", "params": {"chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "names": "null", "dbkey": "\"hg17\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9135", "id": "af3fae2a84d45574", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_unique_seqs.test_tool_000002", "has_data": true}, {"data": {"status": "success", "inputs": {"input|source": "shared", "input|groups": ["forest", "pasture"], "input|calc": ["sharedsobs", "sharedchao"], "input|otu": {"src": "hda", "id": "55d76a6980ecb718"}}, "job": {"inputs": {"otu": {"src": "hda", "id": "55d76a6980ecb718", "uuid": "33113dd2-1063-4523-a1f2-cfc9ba04cf55"}}, "update_time": "2018-02-08T18:54:19.954686", "tool_id": "mothur_venn", "outputs": {"__new_primary_file_unique.sharedsobs.forest-pasture|0.07.sharedchao.forest-pasture__": {"src": "hda", "id": "c306e715ccd40732", "uuid": 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"ff2b605985e5b37e", "uuid": "b0f5b97f-b3d3-4519-93de-91f189d0562d"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.33.sharedsobs.forest-pasture__": {"src": "hda", "id": "a8099d2409335c38", "uuid": "70407edc-f1e2-4892-a83b-4c3d6d52dcd9"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.02.sharedchao.forest-pasture__": {"src": "hda", "id": "99a1f27df53815fe", "uuid": "435d5f82-22de-40ae-9555-c6768884c47f"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.41.sharedsobs.forest-pasture__": {"src": "hda", "id": "5d31cbfd86ba9238", "uuid": "28267b93-9e64-4099-ab3d-9700057dace6"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.14.sharedsobs.forest-pasture__": {"src": "hda", "id": "3c13c8d3678bff11", "uuid": "71fa1471-af01-4a45-9cde-448c4f0ff9ae"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.29.sharedchao.forest-pasture__": {"src": "hda", "id": "b0979d3f12e2ca7c", "uuid": "c0cdaf63-9009-4bd1-b8bb-563612d52ead"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.29.sharedsobs.forest-pasture__": {"src": "hda", "id": "95ebc02141d52b2e", "uuid": "4c6c8f67-65f6-4309-9f9b-288fd4472965"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.12.sharedsobs.forest-pasture__": {"src": "hda", "id": "d44076581aae3b2d", "uuid": "8868b0f7-c31c-4d0e-9b62-a60beab07c48"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.26.sharedchao.forest-pasture__": {"src": "hda", "id": "3809f3db44f7f537", "uuid": "00971f04-a834-44c5-be7d-315e0a75b22c"}, "__new_primary_file_0.55.sharedsobs.forest-pasture|0.27.sharedsobs.forest-pasture__": {"src": "hda", "id": "4726084e39a28c6b", "uuid": "7d8a5eee-c89e-4e14-a228-8c96a6f92e7a"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.41.sharedchao.forest-pasture__": {"src": "hda", "id": "5500dc8db971ab8a", "uuid": "2c1a6f1e-0b8f-47da-974d-383005e13016"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.36.sharedsobs.forest-pasture__": {"src": "hda", "id": 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"__new_primary_file_unique.sharedsobs.forest-pasture|0.15.sharedchao.forest-pasture__": {"src": "hda", "id": "0bd3ae7c57261b58", "uuid": "44ffe1ec-9f86-4159-8976-38d9c96014a7"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.09.sharedchao.forest-pasture__": {"src": "hda", "id": "67a71e47792722f3", "uuid": "b3bdd0fd-2d4d-4b14-9860-ed10dca6779f"}, "__new_primary_file_0.55.sharedsobs.forest-pasture|0.01.sharedsobs.forest-pasture__": {"src": "hda", "id": "b24813383c927074", "uuid": "315b8ad7-a808-4419-b27d-227aa4686931"}, "__new_primary_file_0.55.sharedsobs.forest-pasture|0.02.sharedsobs.forest-pasture__": {"src": "hda", "id": "da17aca212b7e975", "uuid": "8a4464ba-7372-430c-a1d8-9f7e98aa6bc7"}, "__new_primary_file_0.55.sharedsobs.forest-pasture|0.21.sharedsobs.forest-pasture__": {"src": "hda", "id": "0dd63dbbe68f15eb", "uuid": "002ea9f7-1a3e-44a5-820d-b2119ed98732"}, "__new_primary_file_0.55.sharedsobs.forest-pasture|0.12.sharedsobs.forest-pasture__": {"src": "hda", "id": "af254de203595b9a", "uuid": "567e57f9-572f-4983-b64f-3074984a1c20"}, "__new_primary_file_0.55.sharedsobs.forest-pasture|0.23.sharedsobs.forest-pasture__": {"src": "hda", "id": "28bfbd1f682a023c", "uuid": "891629f4-d2fc-481f-827c-39a6498153ed"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.06.sharedsobs.forest-pasture__": {"src": "hda", "id": "037eb00486bbcd0f", "uuid": "e6a36cd8-14e8-4f5e-99ec-97f1da77b706"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.09.sharedsobs.forest-pasture__": {"src": "hda", "id": "605eafdc6b29e694", "uuid": "a989c780-1391-4dfb-b4e2-fb12300181f1"}, "__new_primary_file_0.55.sharedsobs.forest-pasture|0.25.sharedsobs.forest-pasture__": {"src": "hda", "id": "e2ffe484c9600cc9", "uuid": "a1e7f9f4-6eb2-4883-a3d0-5301f5e884ea"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.32.sharedsobs.forest-pasture__": {"src": "hda", "id": "2a3d51fcdfd2c354", "uuid": "4a3fa689-e8f7-4a62-99e5-0ad75b65dea8"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.33.sharedchao.forest-pasture__": {"src": "hda", "id": "f2fcc124cffbfab3", "uuid": "0ee6ba67-680c-424f-9e3b-0565209774b2"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.03.sharedchao.forest-pasture__": {"src": "hda", "id": "1df5bd22b3fa40b7", "uuid": "8c7d429a-c401-4b26-b18d-c829b3166bbf"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.01.sharedsobs.forest-pasture__": {"src": "hda", "id": "eaf5a18433a155d9", "uuid": "254f3491-597c-48b3-829b-83105582f8e5"}, "__new_primary_file_0.55.sharedsobs.forest-pasture|0.03.sharedsobs.forest-pasture__": {"src": "hda", "id": "ae3e576e3ad064fc", "uuid": "dc1f0494-ef72-4e87-bf10-b6552fdb6e19"}, "__new_primary_file_0.55.sharedsobs.forest-pasture|0.19.sharedsobs.forest-pasture__": {"src": "hda", "id": "c6fa67e3e6b69811", "uuid": "abc37e39-abf0-4b89-b866-a97bd798c274"}, "__new_primary_file_0.55.sharedsobs.forest-pasture|0.04.sharedsobs.forest-pasture__": {"src": "hda", "id": "fb2aea7dd0de2197", "uuid": "64a2fc40-6296-4c89-be07-74d8dab70167"}, "__new_primary_file_unique.sharedsobs.forest-pasture|0.19.sharedsobs.forest-pasture__": {"src": "hda", "id": "16059f9897e605d5", "uuid": "6c898ee3-9fe8-4583-a149-835cef0d9dbe"}, "__new_primary_file_0.55.sharedsobs.forest-pasture|0.33.sharedsobs.forest-pasture__": {"src": "hda", "id": "74e0351813a079c6", "uuid": "84464478-e368-48a5-9e29-0cd01802d833"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > venn(shared=input_otu.dat,nseqs=false,permute=4,groups=forest-pasture,c \ralc=sharedsobs-sharedchao,fontsize=24,sharedotus=true)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu.unique.sharedsobs.forest-pasture.svg\ninput_otu.unique.sharedchao.forest-pasture.svg\ninput_otu.0.01.sharedsobs.forest-pasture.svg\ninput_otu.0.01.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.01.sharedchao.forest-pasture.svg\ninput_otu.0.02.sharedsobs.forest-pasture.svg\ninput_otu.0.02.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.02.sharedchao.forest-pasture.svg\ninput_otu.0.03.sharedsobs.forest-pasture.svg\ninput_otu.0.03.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.03.sharedchao.forest-pasture.svg\ninput_otu.0.04.sharedsobs.forest-pasture.svg\ninput_otu.0.04.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.04.sharedchao.forest-pasture.svg\ninput_otu.0.05.sharedsobs.forest-pasture.svg\ninput_otu.0.05.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.05.sharedchao.forest-pasture.svg\ninput_otu.0.06.sharedsobs.forest-pasture.svg\ninput_otu.0.06.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.06.sharedchao.forest-pasture.svg\ninput_otu.0.07.sharedsobs.forest-pasture.svg\ninput_otu.0.07.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.07.sharedchao.forest-pasture.svg\ninput_otu.0.08.sharedsobs.forest-pasture.svg\ninput_otu.0.08.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.08.sharedchao.forest-pasture.svg\ninput_otu.0.09.sharedsobs.forest-pasture.svg\ninput_otu.0.09.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.09.sharedchao.forest-pasture.svg\ninput_otu.0.10.sharedsobs.forest-pasture.svg\ninput_otu.0.10.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.10.sharedchao.forest-pasture.svg\ninput_otu.0.11.sharedsobs.forest-pasture.svg\ninput_otu.0.11.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.11.sharedchao.forest-pasture.svg\ninput_otu.0.12.sharedsobs.forest-pasture.svg\ninput_otu.0.12.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.12.sharedchao.forest-pasture.svg\ninput_otu.0.13.sharedsobs.forest-pasture.svg\ninput_otu.0.13.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.13.sharedchao.forest-pasture.svg\ninput_otu.0.14.sharedsobs.forest-pasture.svg\ninput_otu.0.14.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.14.sharedchao.forest-pasture.svg\ninput_otu.0.15.sharedsobs.forest-pasture.svg\ninput_otu.0.15.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.15.sharedchao.forest-pasture.svg\ninput_otu.0.16.sharedsobs.forest-pasture.svg\ninput_otu.0.16.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.16.sharedchao.forest-pasture.svg\ninput_otu.0.17.sharedsobs.forest-pasture.svg\ninput_otu.0.17.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.17.sharedchao.forest-pasture.svg\ninput_otu.0.18.sharedsobs.forest-pasture.svg\ninput_otu.0.18.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.18.sharedchao.forest-pasture.svg\ninput_otu.0.19.sharedsobs.forest-pasture.svg\ninput_otu.0.19.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.19.sharedchao.forest-pasture.svg\ninput_otu.0.20.sharedsobs.forest-pasture.svg\ninput_otu.0.20.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.20.sharedchao.forest-pasture.svg\ninput_otu.0.21.sharedsobs.forest-pasture.svg\ninput_otu.0.21.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.21.sharedchao.forest-pasture.svg\ninput_otu.0.22.sharedsobs.forest-pasture.svg\ninput_otu.0.22.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.22.sharedchao.forest-pasture.svg\ninput_otu.0.23.sharedsobs.forest-pasture.svg\ninput_otu.0.23.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.23.sharedchao.forest-pasture.svg\ninput_otu.0.24.sharedsobs.forest-pasture.svg\ninput_otu.0.24.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.24.sharedchao.forest-pasture.svg\ninput_otu.0.25.sharedsobs.forest-pasture.svg\ninput_otu.0.25.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.25.sharedchao.forest-pasture.svg\ninput_otu.0.26.sharedsobs.forest-pasture.svg\ninput_otu.0.26.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.26.sharedchao.forest-pasture.svg\ninput_otu.0.27.sharedsobs.forest-pasture.svg\ninput_otu.0.27.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.27.sharedchao.forest-pasture.svg\ninput_otu.0.29.sharedsobs.forest-pasture.svg\ninput_otu.0.29.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.29.sharedchao.forest-pasture.svg\ninput_otu.0.32.sharedsobs.forest-pasture.svg\ninput_otu.0.32.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.32.sharedchao.forest-pasture.svg\ninput_otu.0.33.sharedsobs.forest-pasture.svg\ninput_otu.0.33.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.33.sharedchao.forest-pasture.svg\ninput_otu.0.36.sharedsobs.forest-pasture.svg\ninput_otu.0.36.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.36.sharedchao.forest-pasture.svg\ninput_otu.0.38.sharedsobs.forest-pasture.svg\ninput_otu.0.38.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.38.sharedchao.forest-pasture.svg\ninput_otu.0.41.sharedsobs.forest-pasture.svg\ninput_otu.0.41.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.41.sharedchao.forest-pasture.svg\ninput_otu.0.45.sharedsobs.forest-pasture.svg\ninput_otu.0.45.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.45.sharedchao.forest-pasture.svg\ninput_otu.0.55.sharedsobs.forest-pasture.svg\ninput_otu.0.55.sharedsobs.forest-pasture.sharedotus\ninput_otu.0.55.sharedchao.forest-pasture.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3817.dat' input_otu.dat &&  echo 'venn( shared=input_otu.dat, nseqs=false, permute=4, groups=forest-pasture, calc=sharedsobs-sharedchao, fontsize=24, sharedotus=true )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:54:10.814484", "params": {"sharedotus": "\"true\"", "nseqs": "\"false\"", "dbkey": "\"hg17\"", "fontsize": "\"24\"", "input": "{\"__current_case__\": 0, \"label\": null, \"source\": \"shared\", \"groups\": [\"forest\", \"pasture\"], \"calc\": [\"sharedsobs\", \"sharedchao\"], \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3817}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "permute": "\"4\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by 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"__new_primary_file_.unique.sobs|.0.36.sobs__": {"src": "hda", "id": "06f863c370e9a218", "uuid": "4e126c04-1424-4e31-9746-dbd4430506c4"}, "__new_primary_file_.unique.sobs|.0.16.ace__": {"src": "hda", "id": "7a12ab7b858daf17", "uuid": "507438b3-2a42-4d78-8804-cbf96a2e25a3"}}, "stdout": "\u001b[H\u001b[2J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.\n\nDistributed under the GNU General Public License\n\nType 'help()' for information on the commands that are available\n\nFor questions and analysis support, please visit our forum at https://www.mothur.org/forum\n\nType 'quit()' to exit program\n\n\n\nmothur > venn(list=input_otu.dat,abund=10,calc=sobs-chao-ace,fontsize=24,sharedo \rtus=true)\nunique\n0.01\n0.02\n0.03\n0.04\n0.05\n0.06\n0.07\n0.08\n0.09\n0.10\n0.11\n0.12\n0.13\n0.14\n0.15\n0.16\n0.17\n0.18\n0.19\n0.20\n0.21\n0.22\n0.23\n0.24\n0.25\n0.26\n0.27\n0.29\n0.32\n0.33\n0.36\n0.38\n0.41\n0.45\n0.55\n\nOutput File Names: \ninput_otu..unique.sobs.svg\ninput_otu..unique.chao.svg\ninput_otu..unique.ace.svg\ninput_otu..0.01.sobs.svg\ninput_otu..0.01.chao.svg\ninput_otu..0.01.ace.svg\ninput_otu..0.02.sobs.svg\ninput_otu..0.02.chao.svg\ninput_otu..0.02.ace.svg\ninput_otu..0.03.sobs.svg\ninput_otu..0.03.chao.svg\ninput_otu..0.03.ace.svg\ninput_otu..0.04.sobs.svg\ninput_otu..0.04.chao.svg\ninput_otu..0.04.ace.svg\ninput_otu..0.05.sobs.svg\ninput_otu..0.05.chao.svg\ninput_otu..0.05.ace.svg\ninput_otu..0.06.sobs.svg\ninput_otu..0.06.chao.svg\ninput_otu..0.06.ace.svg\ninput_otu..0.07.sobs.svg\ninput_otu..0.07.chao.svg\ninput_otu..0.07.ace.svg\ninput_otu..0.08.sobs.svg\ninput_otu..0.08.chao.svg\ninput_otu..0.08.ace.svg\ninput_otu..0.09.sobs.svg\ninput_otu..0.09.chao.svg\ninput_otu..0.09.ace.svg\ninput_otu..0.10.sobs.svg\ninput_otu..0.10.chao.svg\ninput_otu..0.10.ace.svg\ninput_otu..0.11.sobs.svg\ninput_otu..0.11.chao.svg\ninput_otu..0.11.ace.svg\ninput_otu..0.12.sobs.svg\ninput_otu..0.12.chao.svg\ninput_otu..0.12.ace.svg\ninput_otu..0.13.sobs.svg\ninput_otu..0.13.chao.svg\ninput_otu..0.13.ace.svg\ninput_otu..0.14.sobs.svg\ninput_otu..0.14.chao.svg\ninput_otu..0.14.ace.svg\ninput_otu..0.15.sobs.svg\ninput_otu..0.15.chao.svg\ninput_otu..0.15.ace.svg\ninput_otu..0.16.sobs.svg\ninput_otu..0.16.chao.svg\ninput_otu..0.16.ace.svg\ninput_otu..0.17.sobs.svg\ninput_otu..0.17.chao.svg\ninput_otu..0.17.ace.svg\ninput_otu..0.18.sobs.svg\ninput_otu..0.18.chao.svg\ninput_otu..0.18.ace.svg\ninput_otu..0.19.sobs.svg\ninput_otu..0.19.chao.svg\ninput_otu..0.19.ace.svg\ninput_otu..0.20.sobs.svg\ninput_otu..0.20.chao.svg\ninput_otu..0.20.ace.svg\ninput_otu..0.21.sobs.svg\ninput_otu..0.21.chao.svg\ninput_otu..0.21.ace.svg\ninput_otu..0.22.sobs.svg\ninput_otu..0.22.chao.svg\ninput_otu..0.22.ace.svg\ninput_otu..0.23.sobs.svg\ninput_otu..0.23.chao.svg\ninput_otu..0.23.ace.svg\ninput_otu..0.24.sobs.svg\ninput_otu..0.24.chao.svg\ninput_otu..0.24.ace.svg\ninput_otu..0.25.sobs.svg\ninput_otu..0.25.chao.svg\ninput_otu..0.25.ace.svg\ninput_otu..0.26.sobs.svg\ninput_otu..0.26.chao.svg\ninput_otu..0.26.ace.svg\ninput_otu..0.27.sobs.svg\ninput_otu..0.27.chao.svg\ninput_otu..0.27.ace.svg\ninput_otu..0.29.sobs.svg\ninput_otu..0.29.chao.svg\ninput_otu..0.29.ace.svg\ninput_otu..0.32.sobs.svg\ninput_otu..0.32.chao.svg\ninput_otu..0.32.ace.svg\ninput_otu..0.33.sobs.svg\ninput_otu..0.33.chao.svg\ninput_otu..0.33.ace.svg\ninput_otu..0.36.sobs.svg\ninput_otu..0.36.chao.svg\ninput_otu..0.36.ace.svg\ninput_otu..0.38.sobs.svg\ninput_otu..0.38.chao.svg\ninput_otu..0.38.ace.svg\ninput_otu..0.41.sobs.svg\ninput_otu..0.41.chao.svg\ninput_otu..0.41.ace.svg\ninput_otu..0.45.sobs.svg\ninput_otu..0.45.chao.svg\ninput_otu..0.45.ace.svg\ninput_otu..0.55.sobs.svg\ninput_otu..0.55.chao.svg\ninput_otu..0.55.ace.svg\n\n\nmothur > quit\n", "command_line": "set -o pipefail;  ln -s '/tmp/saskia/tmpKSDp0p/files/003/dataset_3926.dat' input_otu.dat &&  echo 'venn( list=input_otu.dat, abund=10, calc=sobs-chao-ace, fontsize=24, sharedotus=true )' | sed 's/ //g' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:54:39.400697", "params": {"sharedotus": "\"true\"", "nseqs": "\"false\"", "dbkey": "\"hg17\"", "fontsize": "\"24\"", "input": "{\"abund\": \"10\", \"label\": null, \"source\": \"similarity\", \"__current_case__\": 1, \"calc\": [\"sobs\", \"chao\", \"ace\"], \"otu\": {\"values\": [{\"src\": \"hda\", \"id\": 3926}]}}", "chromInfo": "\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\"", "permute": "\"4\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\n", "job_metrics": [], "model_class": "Job", "external_id": "9316", "id": "ec7711f2346cbca2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_venn.test_tool_000001", "has_data": true}], "version": "0.1", "exit_code": 1, "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 1, "num_tests": 305}};
-        renderTestResults(test_data);
-      }
-    </script>
-  </body>
-</html>
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