Mercurial > repos > fubar > rgrnastar_203e

changeset 27:78f015992ac6 draft

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Uploaded
author fubar
date Fri, 06 Mar 2015 17:22:18 -0500
parents 79a6af1a7c79
children cde7cee8cfd0
files .shed.yml rg_rnaStar.xml tool_test_output.json
diffstat 3 files changed, 5 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Fri Mar 06 17:22:18 2015 -0500
@@ -0,0 +1,3 @@
+# repository published to https://testtoolshed.g2.bx.psu.edu/repos/fubar/rgrnastar_203e
+owner: fubar
+name: rgrnastar_203e
--- a/rg_rnaStar.xml	Thu Feb 26 22:41:22 2015 -0500
+++ b/rg_rnaStar.xml	Fri Mar 06 17:22:18 2015 -0500
@@ -24,7 +24,7 @@
     #if str($refGenomeSource.genomeSource) == 'history':
         --genomeDir "tempstargenomedir"
     #else
-        --genomeDir $refGenomeSource.index.fields.pathls 
+        --genomeDir $refGenomeSource.index.fields.path 
     #end if
     --readFilesIn $singlePaired.input1 
     #if str($singlePaired.sPaired) == "paired"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_test_output.json	Fri Mar 06 17:22:18 2015 -0500
@@ -0,0 +1,1 @@
+{"tests": [{"data": {"status": "failure", "inputs": {"outSAMstrandField": "--outSAMstrandField intronMotif", "outSAMattributes": "--outSAMattributes All", "singlePaired|sPaired": "single", "singlePaired|input1": {"src": "hda", "id": "2891970512fa2d5a"}, "refGenomeSource|genomeSource": "history", "refGenomeSource|ownFile": {"src": "hda", "id": "5729865256bc2525"}, "jobName": "rnastar_test", "outFilterIntronMotifs": "--outFilterIntronMotifs RemoveNoncanonical"}, "output_problems": ["[Errno 2] No such file or directory: '/var/lib/jenkins/workspace/TTS-Pusher/tools/rgrnastar_240d/test-data/rnastar_test.log'", "Files /tmp/tmpLmml3V/tmp/tmp3miAl7rnastar_test_mapped_reads.bam=92b but /var/lib/jenkins/workspace/TTS-Pusher/tools/rgrnastar_240d/test-data/rnastar_test_mapped_reads.bam=3877b - compare (delta=200) failed"], "job": {"inputs": {"input1": {"src": "hda", "id": "2891970512fa2d5a"}, "ownFile": {"src": "hda", "id": "5729865256bc2525"}}, "update_time": "2015-02-18T15:43:05.328891", "tool_id": "rna_star", "outputs": {"output_log": {"src": "hda", "id": "54f2a3a23292eb07"}, "splice_junctions": {"src": "hda", "id": "8155e4b4bf1581ff"}, "mapped_reads": {"src": "hda", "id": "7b55dbb89df8f4e5"}}, "stdout": "Warning: Some stderr/stdout text\n", "command_line": "mkdir -p tempstargenomedir; STAR --runMode genomeGenerate --genomeDir \"tempstargenomedir\" --genomeFastaFiles \"/tmp/tmpLmml3Vfiles/000/dataset_2.dat\" --runThreadN 2 ; STAR --genomeLoad NoSharedMemory --genomeDir \"tempstargenomedir\" --readFilesIn /tmp/tmpLmml3Vfiles/000/dataset_1.dat --runThreadN 4  --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMattributes All  ;  samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2>/dev/null", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T15:42:58.094458", "params": {"outSAMstrandField": "\"--outSAMstrandField intronMotif\"", "singlePaired": "{\"sPaired\": \"single\", \"input1\": 1, \"__current_case__\": 0}", "chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "outSAMattributes": "\"--outSAMattributes All\"", "dbkey": "\"hg17\"", "jobName": "\"rnastar_test\"", "params": "{\"settingsType\": \"preSet\", \"__current_case__\": 0}", "refGenomeSource": "{\"genomeSource\": \"history\", \"ownFile\": 2, \"__current_case__\": 1, \"geneModel\": null}", "outFilterIntronMotifs": "\"--outFilterIntronMotifs RemoveNoncanonical\""}, "stderr": "Warning: Some stderr/stdout text\n/tmp/tmpLmml3V/job_working_directory/000/3/galaxy_3.sh: 20: /tmp/tmpLmml3V/job_working_directory/000/3/galaxy_3.sh: STAR: not found\n/tmp/tmpLmml3V/job_working_directory/000/3/galaxy_3.sh: 20: /tmp/tmpLmml3V/job_working_directory/000/3/galaxy_3.sh: STAR: not found\n[E::hts_open] fail to open file 'Aligned.out.sam'\nsamtools: failed to open \"Aligned.out.sam\" for reading: No such file or directory\n", "job_metrics": [], "model_class": "Job", "external_id": "10175", "id": "54f2a3a23292eb07", "user_email": "test@bx.psu.edu"}, "problem_log": "Traceback (most recent call last):\n  File \"/usr/lib/python2.7/unittest/case.py\", line 331, in run\n    testMethod()\n  File \"/var/lib/jenkins/galaxy/default/test/functional/test_toolbox.py\", line 268, in test_tool\n    self.do_it( td )\n  File \"/var/lib/jenkins/galaxy/default/test/functional/test_toolbox.py\", line 67, in do_it\n    raise e\nJobOutputsError: [Errno 2] No such file or directory: '/var/lib/jenkins/workspace/TTS-Pusher/tools/rgrnastar_240d/test-data/rnastar_test.log'\nFiles /tmp/tmpLmml3V/tmp/tmp3miAl7rnastar_test_mapped_reads.bam=92b but /var/lib/jenkins/workspace/TTS-Pusher/tools/rgrnastar_240d/test-data/rnastar_test_mapped_reads.bam=3877b - compare (delta=200) failed\n-------------------- >> begin captured logging << --------------------\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nurllib3.connectionpool: DEBUG: \"GET /api/users?key=test_key HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nurllib3.connectionpool: DEBUG: \"POST /api/users HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nurllib3.connectionpool: DEBUG: \"POST /api/users/2891970512fa2d5a/api_key HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"POST /api/histories HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1\nurllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.jobs: DEBUG: (1) Working directory for job is: /tmp/tmpLmml3V/job_working_directory/000/1\ngalaxy.jobs.handler: DEBUG: (1) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (1) Job dispatched\ngalaxy.jobs.runners: DEBUG: (1) command is: python /var/lib/jenkins/galaxy/default/tools/data_source/upload.py /var/lib/jenkins/galaxy/default /tmp/tmpLmml3V/tmp/tmp4Cqjv7 /tmp/tmpLmml3V/tmp/tmphQMjTa 1:/tmp/tmpLmml3V/job_working_directory/000/1/dataset_1_files:/tmp/tmpLmml3Vfiles/000/dataset_1.dat; return_code=$?; cd /var/lib/jenkins/galaxy/default; /var/lib/jenkins/galaxy/default/set_metadata.sh /tmp/tmpLmml3Vfiles /tmp/tmpLmml3V/job_working_directory/000/1 . /tmp/tmp7csU5U/functional_tests_wsgi.ini /tmp/tmpLmml3V/tmp/tmp4Cqjv7 /tmp/tmpLmml3V/job_working_directory/000/1/galaxy.json /tmp/tmpLmml3V/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_38l_xc,/tmp/tmpLmml3V/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_9_jGgQ,/tmp/tmpLmml3V/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_UXEuRV,/tmp/tmpLmml3V/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1__HnZz3,,/tmp/tmpLmml3V/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_bHILGD; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/tmpLmml3V/job_working_directory/000/1/galaxy_1.sh\ngalaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpLmml3V/job_working_directory/000/1/galaxy_1.sh\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 1\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.jobs: DEBUG: job 1 ended\ngalaxy.tools.actions.upload_common: INFO: tool upload1 created job id 2\nurllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/tmpLmml3V/job_working_directory/000/2\ngalaxy.jobs.handler: DEBUG: (2) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (2) Job dispatched\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.jobs.runners: DEBUG: (2) command is: python /var/lib/jenkins/galaxy/default/tools/data_source/upload.py /var/lib/jenkins/galaxy/default /tmp/tmpLmml3V/tmp/tmp4Cqjv7 /tmp/tmpLmml3V/tmp/tmpxhbiAn 2:/tmp/tmpLmml3V/job_working_directory/000/2/dataset_2_files:/tmp/tmpLmml3Vfiles/000/dataset_2.dat; return_code=$?; cd /var/lib/jenkins/galaxy/default; /var/lib/jenkins/galaxy/default/set_metadata.sh /tmp/tmpLmml3Vfiles /tmp/tmpLmml3V/job_working_directory/000/2 . /tmp/tmp7csU5U/functional_tests_wsgi.ini /tmp/tmpLmml3V/tmp/tmp4Cqjv7 /tmp/tmpLmml3V/job_working_directory/000/2/galaxy.json /tmp/tmpLmml3V/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_O3AlYB,/tmp/tmpLmml3V/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_rUMEUW,/tmp/tmpLmml3V/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_dUnESE,/tmp/tmpLmml3V/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_i6UkVa,,/tmp/tmpLmml3V/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_jz89yn; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/tmpLmml3V/job_working_directory/000/2/galaxy_2.sh\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpLmml3V/job_working_directory/000/2/galaxy_2.sh\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 2\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.jobs: DEBUG: job 2 ended\ngalaxy.util.object_wrapper: WARNING: Unable to create dynamic subclass for <type 'instance'>, None: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases\ngalaxy.jobs: DEBUG: (3) Working directory for job is: /tmp/tmpLmml3V/job_working_directory/000/3\ngalaxy.jobs.handler: DEBUG: (3) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (3) Job dispatched\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\ngalaxy.jobs.runners: DEBUG: (3) command is: mkdir -p tempstargenomedir; STAR --runMode genomeGenerate --genomeDir \"tempstargenomedir\" --genomeFastaFiles \"/tmp/tmpLmml3Vfiles/000/dataset_2.dat\" --runThreadN 2 ; STAR --genomeLoad NoSharedMemory --genomeDir \"tempstargenomedir\" --readFilesIn /tmp/tmpLmml3Vfiles/000/dataset_1.dat --runThreadN 4  --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMattributes All  ;  samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2>/dev/null; return_code=$?; if [ -f /tmp/tmpLmml3V/job_working_directory/000/3/Log.final.out ] ; then cp /tmp/tmpLmml3V/job_working_directory/000/3/Log.final.out /tmp/tmpLmml3Vfiles/000/dataset_3.dat ; fi; if [ -f /tmp/tmpLmml3V/job_working_directory/000/3/SJ.out.tab ] ; then cp /tmp/tmpLmml3V/job_working_directory/000/3/SJ.out.tab /tmp/tmpLmml3Vfiles/000/dataset_4.dat ; fi; if [ -f /tmp/tmpLmml3V/job_working_directory/000/3/AlignedSorted.bam ] ; then cp /tmp/tmpLmml3V/job_working_directory/000/3/AlignedSorted.bam /tmp/tmpLmml3Vfiles/000/dataset_5.dat ; fi; cd /var/lib/jenkins/galaxy/default; /var/lib/jenkins/galaxy/default/set_metadata.sh /tmp/tmpLmml3Vfiles /tmp/tmpLmml3V/job_working_directory/000/3 . /tmp/tmp7csU5U/functional_tests_wsgi.ini /tmp/tmpLmml3V/tmp/tmp4Cqjv7 /tmp/tmpLmml3V/job_working_directory/000/3/galaxy.json /tmp/tmpLmml3V/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_3_mo4KmW,/tmp/tmpLmml3V/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_Lii6lg,/tmp/tmpLmml3V/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_3_Qfosnw,/tmp/tmpLmml3V/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_3_bAWKm3,,/tmp/tmpLmml3V/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_3_JMuyFE /tmp/tmpLmml3V/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_4_vlfKtW,/tmp/tmpLmml3V/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_4_vHf_0G,/tmp/tmpLmml3V/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_4_noAoJL,/tmp/tmpLmml3V/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_4_H8l4_n,,/tmp/tmpLmml3V/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_4_yOYn0W /tmp/tmpLmml3V/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_5_K7TDge,/tmp/tmpLmml3V/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_5_TNrn8m,/tmp/tmpLmml3V/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_5_1ZpsjQ,/tmp/tmpLmml3V/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_5_GzbL0L,,/tmp/tmpLmml3V/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_5_mn8ziY; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (3) executing job script: /tmp/tmpLmml3V/job_working_directory/000/3/galaxy_3.sh\ngalaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpLmml3V/job_working_directory/000/3/galaxy_3.sh\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\ngalaxy.jobs.output_checker: INFO: Job 3: Warning: Some stderr/stdout text\ngalaxy.jobs.output_checker: INFO: Job 3: Warning: Some stderr/stdout text\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 5\ngalaxy.jobs: DEBUG: job 3 ended\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?full=true&key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/display?raw=true&key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmpLmml3V/jobfiles, ofn: /tmp/tmpLmml3V/jobfiles/rnastar_test.log\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmpLmml3V/jobfiles. saved /tmp/tmpLmml3V/jobfiles/rnastar_test.log\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/display?raw=true&key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmpLmml3V/jobfiles, ofn: /tmp/tmpLmml3V/jobfiles/rnastar_test_splicejunctions.bed\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmpLmml3V/jobfiles. saved /tmp/tmpLmml3V/jobfiles/rnastar_test_splicejunctions.bed\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/display?raw=true&key=9a816550b4431c71406fb7305c8248f3 HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmpLmml3V/jobfiles, ofn: /tmp/tmpLmml3V/jobfiles/rnastar_test_mapped_reads.bam\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmpLmml3V/jobfiles. saved /tmp/tmpLmml3V/jobfiles/rnastar_test_mapped_reads.bam\n--------------------- >> end captured logging << ---------------------\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_rna_star.test_tool_000000", "has_data": true}], "version": "0.1", "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 1, "num_tests": 1}}
\ No newline at end of file