view tool_test_output.json @ 36:8c8ae1e19b10 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a

{"tests": [{"data": {"status": "success", "inputs": {"LVL2MAXGAP": "800", "LVL1MAXGAP": "30", "minlen": "200", "cutofflink": "1.0", "cutoffpeak": "2.0", "infile": {"src": "hda", "id": "2891970512fa2d5a"}}, "job": {"inputs": {"infile": {"src": "hda", "id": "2891970512fa2d5a"}}, "update_time": "2015-02-18T15:43:32.598593", "tool_id": "macs2_bdgbroadcall", "outputs": {"outfile": {"src": "hda", "id": "5729865256bc2525"}}, "stdout": "", "command_line": "macs2 bdgbroadcall --ifile \"/tmp/tmpU7WkCtfiles/000/dataset_1.dat\" --cutoff-peak \"2.0\" --cutoff-link \"1.0\" --min-length \"200\" --lvl1-max-gap \"30\" --lvl2-max-gap \"800\" --ofile \"macs2_bdgbroadcall.bdg\" && awk '!/^track name/' \"macs2_bdgbroadcall.bdg\" > \"/tmp/tmpU7WkCtfiles/000/dataset_2.dat\"", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T15:43:28.095378", "params": {"LVL2MAXGAP": "\"800\"", "LVL1MAXGAP": "\"30\"", "minlen": "\"200\"", "chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\"", "cutofflink": "\"1.0\"", "cutoffpeak": "\"2.0\""}, "stderr": "INFO  @ Wed, 18 Feb 2015 10:43:29: Read and build bedGraph... \nINFO  @ Wed, 18 Feb 2015 10:43:29: Call peaks from bedGraph... \nINFO  @ Wed, 18 Feb 2015 10:43:29: Write peaks... \nINFO  @ Wed, 18 Feb 2015 10:43:29: Done \n", "job_metrics": [], "model_class": "Job", "external_id": "10263", "id": "5729865256bc2525", "user_email": "[e-mail]"}}, "id": "functional.test_toolbox.TestForTool_macs2_bdgbroadcall.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"infile_control": {"src": "hda", "id": "8155e4b4bf1581ff"}, "bdgcmp_options|bdgcmp_options_selector": "slogLR", "infile_treatment": {"src": "hda", "id": "54f2a3a23292eb07"}}, "job": {"inputs": {"infile_control": {"src": "hda", "id": "8155e4b4bf1581ff"}, "infile_treatment": {"src": "hda", "id": "54f2a3a23292eb07"}}, "update_time": "2015-02-18T15:44:02.998290", "tool_id": "macs2_bdgcmp", "outputs": {"outfile": {"src": "hda", "id": "7b55dbb89df8f4e5"}}, "stdout": "", "command_line": "macs2 bdgcmp -t \"/tmp/tmpU7WkCtfiles/000/dataset_3.dat\" -c \"/tmp/tmpU7WkCtfiles/000/dataset_4.dat\"  -m \"slogLR\" -o \"/tmp/tmpU7WkCtfiles/000/dataset_5.dat\"", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T15:43:55.560276", "params": {"chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "bdgcmp_options": "{\"bdgcmp_options_selector\": \"slogLR\", \"__current_case__\": 6}", "dbkey": "\"hg17\""}, "stderr": "INFO  @ Wed, 18 Feb 2015 10:43:58: Read and build treatment bedGraph... \nINFO  @ Wed, 18 Feb 2015 10:43:58: Read and build control bedGraph... \nINFO  @ Wed, 18 Feb 2015 10:43:58: Build scoreTrackII... \nINFO  @ Wed, 18 Feb 2015 10:43:58: Calculate scores comparing treatment and control by 'slogLR'... \nINFO  @ Wed, 18 Feb 2015 10:43:58: Write bedGraph of scores... \nINFO  @ Wed, 18 Feb 2015 10:43:58: Finished 'slogLR'! Please check '/tmp/tmpU7WkCtfiles/000/dataset_5.dat'! \n", "job_metrics": [], "model_class": "Job", "external_id": "10304", "id": "7b55dbb89df8f4e5", "user_email": "[e-mail]"}}, "id": "functional.test_toolbox.TestForTool_macs2_bdgcmp.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"maxgap": "30", "cutoff": "5.0", "infile": {"src": "hda", "id": "fa6d20d0fb68383f"}, "minlen": "200"}, "job": {"inputs": {"infile": {"src": "hda", "id": "fa6d20d0fb68383f"}}, "update_time": "2015-02-18T15:44:23.995434", "tool_id": "macs2_bdgpeakcall", "outputs": {"outfile": {"src": "hda", "id": "683bc220e21425bb"}}, "stdout": "", "command_line": "macs2 bdgpeakcall --ifile \"/tmp/tmpU7WkCtfiles/000/dataset_6.dat\" --cutoff \"5.0\" --min-length \"200\" --max-gap \"30\"  --no-trackline --ofile \"macs2_bdgpeakcall.bdg\" && awk '!/^track name/' \"macs2_bdgpeakcall.bdg\" > \"/tmp/tmpU7WkCtfiles/000/dataset_7.dat\"", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T15:44:17.768604", "params": {"cutoff": "\"5.0\"", "notrackline": "\"False\"", "maxgap": "\"30\"", "minlen": "\"200\"", "dbkey": "\"hg17\"", "callsummits": "\"False\"", "chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "INFO  @ Wed, 18 Feb 2015 10:44:19: Read and build bedGraph... \nINFO  @ Wed, 18 Feb 2015 10:44:19: Call peaks from bedGraph... \nINFO  @ Wed, 18 Feb 2015 10:44:19: Write peaks... \nINFO  @ Wed, 18 Feb 2015 10:44:19: Done \n", "job_metrics": [], "model_class": "Job", "external_id": "10348", "id": "683bc220e21425bb", "user_email": "[e-mail]"}}, "id": "functional.test_toolbox.TestForTool_macs2_bdgpeakcall.test_tool_000000", "has_data": true}, {"data": {"status": "failure", "inputs": {"effective_genome_size_options|gsize": "3300000000", "cutoff_options|cutoff_options_selector": "qvalue", "outputs": ["peaks_bed", "bdg"], "input_treatment_file": {"src": "hda", "id": "a90a30fafe298e1e"}, "effective_genome_size_options|effective_genome_size_options_selector": "user_defined", "input_control_file": {"src": "hda", "id": "b842d972534ccb3e"}, "cutoff_options|qvalue": "0.05", "band_width": "300"}, "output_problems": ["History item  different than expected, difference (using contains):\n( /var/lib/jenkins/workspace/TTS-Pusher/tools/macs2/test-data/callpeak_part.bed v. /tmp/tmpU7WkCt/tmp/tmpgwWvfAcallpeak_part.bed )\nFailed to find 'chr1\t840081\t840400\t319\t840240\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_1' in history data. (lines_diff=0):\n", "History item  different than expected, difference (using contains):\n( /var/lib/jenkins/workspace/TTS-Pusher/tools/macs2/test-data/callpeak_summits_part.bed v. /tmp/tmpU7WkCt/tmp/tmpdoP9zicallpeak_summits_part.bed )\nFailed to find 'chr1\t840239\t840240\tMACS2_peak_1\t7.51487' in history data. (lines_diff=0):\n"], "job": {"inputs": {"input_control_file": {"src": "hda", "id": "b842d972534ccb3e"}, "input_treatment_file": {"src": "hda", "id": "a90a30fafe298e1e"}}, "update_time": "2015-02-18T15:45:45.787264", "tool_id": "macs2_callpeak", "outputs": {"output_control_lambda": {"src": "hda", "id": "b54fb481e575bccc"}, "output_treat_pileup": {"src": "hda", "id": "80b8022ff3f677b7"}, "output_bed": {"src": "hda", "id": "5449172d6ff5669b"}, "output_narrowpeaks": {"src": "hda", "id": "9ce08b2254e4d5ed"}}, "stdout": "INFO  @ Wed, 18 Feb 2015 10:45:05: \n# Command line: callpeak --name MACS2 -t /tmp/tmpU7WkCtfiles/000/dataset_8.dat -c /tmp/tmpU7WkCtfiles/000/dataset_9.dat --format=BED --gsize 3300000000 --bw=300 --bdg --qvalue 0.05\n# ARGUMENTS LIST:\n# name = MACS2\n# format = BED\n# ChIP-seq file = ['/tmp/tmpU7WkCtfiles/000/dataset_8.dat']\n# control file = ['/tmp/tmpU7WkCtfiles/000/dataset_9.dat']\n# effective genome size = 3.30e+09\n# band width = 300\n# model fold = [5, 50]\n# qvalue cutoff = 5.00e-02\n# Larger dataset will be scaled towards smaller dataset.\n# Range for calculating regional lambda is: 1000 bps and 10000 bps\n# Broad region calling is off\n \nINFO  @ Wed, 18 Feb 2015 10:45:05: #1 read tag files... \nINFO  @ Wed, 18 Feb 2015 10:45:05: #1 read treatment tags... \nINFO  @ Wed, 18 Feb 2015 10:45:05: #1.2 read input tags... \nINFO  @ Wed, 18 Feb 2015 10:45:06: #1 tag size is determined as 100 bps \nINFO  @ Wed, 18 Feb 2015 10:45:06: #1 tag size = 100 \nINFO  @ Wed, 18 Feb 2015 10:45:06: #1  total tags in treatment: 199977 \nINFO  @ Wed, 18 Feb 2015 10:45:06: #1 user defined the maximum tags... \nINFO  @ Wed, 18 Feb 2015 10:45:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) \nINFO  @ Wed, 18 Feb 2015 10:45:06: #1  tags after filtering in treatment: 199583 \nINFO  @ Wed, 18 Feb 2015 10:45:06: #1  Redundant rate of treatment: 0.00 \nINFO  @ Wed, 18 Feb 2015 10:45:06: #1  total tags in control: 199978 \nINFO  @ Wed, 18 Feb 2015 10:45:06: #1 user defined the maximum tags... \nINFO  @ Wed, 18 Feb 2015 10:45:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) \nINFO  @ Wed, 18 Feb 2015 10:45:06: #1  tags after filtering in control: 199867 \nINFO  @ Wed, 18 Feb 2015 10:45:06: #1  Redundant rate of control: 0.00 \nINFO  @ Wed, 18 Feb 2015 10:45:06: #1 finished! \nINFO  @ Wed, 18 Feb 2015 10:45:06: #2 Build Peak Model... \nINFO  @ Wed, 18 Feb 2015 10:45:06: #2 number of paired peaks: 4494 \nINFO  @ Wed, 18 Feb 2015 10:45:06: start model_add_line... \nINFO  @ Wed, 18 Feb 2015 10:45:07: start X-correlation... \nINFO  @ Wed, 18 Feb 2015 10:45:07: end of X-cor \nINFO  @ Wed, 18 Feb 2015 10:45:07: #2 finished! \nINFO  @ Wed, 18 Feb 2015 10:45:07: #2 predicted fragment length is 254 bps \nINFO  @ Wed, 18 Feb 2015 10:45:07: #2 alternative fragment length(s) may be 254 bps \nINFO  @ Wed, 18 Feb 2015 10:45:07: #2.2 Generate R script for model : MACS2_model.r \nINFO  @ Wed, 18 Feb 2015 10:45:07: #3 Call peaks... \nINFO  @ Wed, 18 Feb 2015 10:45:07: #3 Pre-compute pvalue-qvalue table... \nINFO  @ Wed, 18 Feb 2015 10:45:11: #3 In the peak calling step, the following will be performed simultaneously: \nINFO  @ Wed, 18 Feb 2015 10:45:11: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... MACS2_treat_pileup.bdg \nINFO  @ Wed, 18 Feb 2015 10:45:11: #3   Write bedGraph files for control lambda (after scaling if necessary)... MACS2_control_lambda.bdg \nINFO  @ Wed, 18 Feb 2015 10:45:11: #3   Pileup will be based on sequencing depth in treatment. \nINFO  @ Wed, 18 Feb 2015 10:45:11: #3 Call peaks for each chromosome... \nINFO  @ Wed, 18 Feb 2015 10:45:35: #4 Write output xls file... MACS2_peaks.xls \nINFO  @ Wed, 18 Feb 2015 10:45:35: #4 Write peak in narrowPeak format file... MACS2_peaks.narrowPeak \nINFO  @ Wed, 18 Feb 2015 10:45:35: #4 Write summits bed file... MACS2_summits.bed \nINFO  @ Wed, 18 Feb 2015 10:45:35: Done! \n", "command_line": "(macs2 callpeak  --name \"MACS2\" -t \"/tmp/tmpU7WkCtfiles/000/dataset_8.dat\"  -c \"/tmp/tmpU7WkCtfiles/000/dataset_9.dat\"  --format='BED'   --gsize \"3300000000\"   --bw='300'   --bdg  --qvalue \"0.05\"   2> macs2_stderr) && awk '$2-=1' MACS2_peaks.xls | awk '!/^#/' | awk -v OFS='\\t' '$1=$1' | tail -n+3  > \"/tmp/tmpU7WkCtfiles/000/dataset_10.dat\"   ; exit_code_for_galaxy=$?; cat macs2_stderr 2>&1; (exit $exit_code_for_galaxy)", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T15:45:02.829940", "params": {"effective_genome_size_options": "{\"gsize\": \"3300000000\", \"effective_genome_size_options_selector\": \"user_defined\", \"__current_case__\": 0}", "bampe": "\"False\"", "outputs": "[\"peaks_bed\", \"bdg\"]", "cutoff_options": "{\"cutoff_options_selector\": \"qvalue\", \"qvalue\": \"0.05\", \"__current_case__\": 1}", "advanced_options": "{\"advanced_options_selector\": \"off\", \"__current_case__\": 1}", "dbkey": "\"hg17\"", "nomodel_type": "{\"nomodel_type_selector\": \"create_model\", \"__current_case__\": 0}", "chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "band_width": "\"300\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "10410", "id": "5449172d6ff5669b", "user_email": "[e-mail]"}, "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: History item  different than expected, difference (using contains):\n( /var/lib/jenkins/workspace/TTS-Pusher/tools/macs2/test-data/callpeak_part.bed v. /tmp/tmpU7WkCt/tmp/tmpgwWvfAcallpeak_part.bed )\nFailed to find 'chr1\t840081\t840400\t319\t840240\t4.00\t11.15252\t4.92435\t7.51487\tMACS2_peak_1' in history data. (lines_diff=0):\n\nHistory item  different than expected, difference (using contains):\n( /var/lib/jenkins/workspace/TTS-Pusher/tools/macs2/test-data/callpeak_summits_part.bed v. /tmp/tmpU7WkCt/tmp/tmpdoP9zicallpeak_summits_part.bed )\nFailed to find 'chr1\t840239\t840240\tMACS2_peak_1\t7.51487' in history data. (lines_diff=0):\n\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/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 8\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: (8) Working directory for job is: /tmp/tmpU7WkCt/job_working_directory/000/8\ngalaxy.jobs.handler: DEBUG: (8) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/histories/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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: (8) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (8) Job dispatched\nurllib3.connectionpool: DEBUG: \"GET /api/histories/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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: (8) command is: python /var/lib/jenkins/galaxy/default/tools/data_source/upload.py /var/lib/jenkins/galaxy/default /tmp/tmpU7WkCt/tmp/tmpJBkl_S /tmp/tmpU7WkCt/tmp/tmpXiASR3 8:/tmp/tmpU7WkCt/job_working_directory/000/8/dataset_8_files:/tmp/tmpU7WkCtfiles/000/dataset_8.dat; return_code=$?; cd /var/lib/jenkins/galaxy/default; /var/lib/jenkins/galaxy/default/set_metadata.sh /tmp/tmpU7WkCtfiles /tmp/tmpU7WkCt/job_working_directory/000/8 . /tmp/tmpsnDH3q/functional_tests_wsgi.ini /tmp/tmpU7WkCt/tmp/tmpJBkl_S /tmp/tmpU7WkCt/job_working_directory/000/8/galaxy.json /tmp/tmpU7WkCt/job_working_directory/000/8/metadata_in_HistoryDatasetAssociation_8_ZpIxVy,/tmp/tmpU7WkCt/job_working_directory/000/8/metadata_kwds_HistoryDatasetAssociation_8_GWevKA,/tmp/tmpU7WkCt/job_working_directory/000/8/metadata_out_HistoryDatasetAssociation_8_w2AP97,/tmp/tmpU7WkCt/job_working_directory/000/8/metadata_results_HistoryDatasetAssociation_8_tNSXAj,,/tmp/tmpU7WkCt/job_working_directory/000/8/metadata_override_HistoryDatasetAssociation_8_6QVBJk; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (8) executing job script: /tmp/tmpU7WkCt/job_working_directory/000/8/galaxy_8.sh\ngalaxy.jobs: DEBUG: (8) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: DEBUG: \"GET /api/histories/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpU7WkCt/job_working_directory/000/8/galaxy_8.sh\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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 8\nurllib3.connectionpool: DEBUG: \"GET /api/histories/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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 8 ended\ngalaxy.tools.actions.upload_common: INFO: tool upload1 created job id 9\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: (9) Working directory for job is: /tmp/tmpU7WkCt/job_working_directory/000/9\ngalaxy.jobs.handler: DEBUG: (9) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/histories/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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: (9) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (9) Job dispatched\nurllib3.connectionpool: DEBUG: \"GET /api/histories/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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: (9) command is: python /var/lib/jenkins/galaxy/default/tools/data_source/upload.py /var/lib/jenkins/galaxy/default /tmp/tmpU7WkCt/tmp/tmpJBkl_S /tmp/tmpU7WkCt/tmp/tmp2xKzSr 9:/tmp/tmpU7WkCt/job_working_directory/000/9/dataset_9_files:/tmp/tmpU7WkCtfiles/000/dataset_9.dat; return_code=$?; cd /var/lib/jenkins/galaxy/default; /var/lib/jenkins/galaxy/default/set_metadata.sh /tmp/tmpU7WkCtfiles /tmp/tmpU7WkCt/job_working_directory/000/9 . /tmp/tmpsnDH3q/functional_tests_wsgi.ini /tmp/tmpU7WkCt/tmp/tmpJBkl_S /tmp/tmpU7WkCt/job_working_directory/000/9/galaxy.json /tmp/tmpU7WkCt/job_working_directory/000/9/metadata_in_HistoryDatasetAssociation_9_BLCSWi,/tmp/tmpU7WkCt/job_working_directory/000/9/metadata_kwds_HistoryDatasetAssociation_9_7Gdfq9,/tmp/tmpU7WkCt/job_working_directory/000/9/metadata_out_HistoryDatasetAssociation_9_OOFnKe,/tmp/tmpU7WkCt/job_working_directory/000/9/metadata_results_HistoryDatasetAssociation_9_Omnsyx,,/tmp/tmpU7WkCt/job_working_directory/000/9/metadata_override_HistoryDatasetAssociation_9_u8mvPW; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (9) executing job script: /tmp/tmpU7WkCt/job_working_directory/000/9/galaxy_9.sh\nurllib3.connectionpool: DEBUG: \"GET /api/histories/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: (9) Persisting job destination (destination id: local:///)\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpU7WkCt/job_working_directory/000/9/galaxy_9.sh\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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 9\nurllib3.connectionpool: DEBUG: \"GET /api/histories/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff?key=d901781e67b8bb0595a0acef05cb2221 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 9 ended\ngalaxy.jobs: DEBUG: (10) Working directory for job is: /tmp/tmpU7WkCt/job_working_directory/000/10\ngalaxy.jobs.handler: DEBUG: (10) 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/5449172d6ff5669b?key=d901781e67b8bb0595a0acef05cb2221 HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: (10) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (10) 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/5449172d6ff5669b?key=d901781e67b8bb0595a0acef05cb2221 HTTP/1.1\" 200 None\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\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5449172d6ff5669b?key=d901781e67b8bb0595a0acef05cb2221 HTTP/1.1\" 200 None\ngalaxy.jobs.runners: DEBUG: (10) command is: macs2 --version > /tmp/tmpU7WkCt/tmp/GALAXY_VERSION_STRING_10 2>&1; (macs2 callpeak  --name \"MACS2\" -t \"/tmp/tmpU7WkCtfiles/000/dataset_8.dat\"  -c \"/tmp/tmpU7WkCtfiles/000/dataset_9.dat\"  --format='BED'   --gsize \"3300000000\"   --bw='300'   --bdg  --qvalue \"0.05\"   2> macs2_stderr) && awk '$2-=1' MACS2_peaks.xls | awk '!/^#/' | awk -v OFS='\\t' '$1=$1' | tail -n+3  > \"/tmp/tmpU7WkCtfiles/000/dataset_10.dat\"   ; exit_code_for_galaxy=$?; cat macs2_stderr 2>&1; (exit $exit_code_for_galaxy); return_code=$?; if [ -f /tmp/tmpU7WkCt/job_working_directory/000/10/MACS2_peaks.narrowPeak ] ; then cp /tmp/tmpU7WkCt/job_working_directory/000/10/MACS2_peaks.narrowPeak /tmp/tmpU7WkCtfiles/000/dataset_11.dat ; fi; if [ -f /tmp/tmpU7WkCt/job_working_directory/000/10/MACS2_treat_pileup.bdg ] ; then cp /tmp/tmpU7WkCt/job_working_directory/000/10/MACS2_treat_pileup.bdg /tmp/tmpU7WkCtfiles/000/dataset_12.dat ; fi; if [ -f /tmp/tmpU7WkCt/job_working_directory/000/10/MACS2_control_lambda.bdg ] ; then cp /tmp/tmpU7WkCt/job_working_directory/000/10/MACS2_control_lambda.bdg /tmp/tmpU7WkCtfiles/000/dataset_13.dat ; fi; cd /var/lib/jenkins/galaxy/default; /var/lib/jenkins/galaxy/default/set_metadata.sh /tmp/tmpU7WkCtfiles /tmp/tmpU7WkCt/job_working_directory/000/10 . /tmp/tmpsnDH3q/functional_tests_wsgi.ini /tmp/tmpU7WkCt/tmp/tmpJBkl_S /tmp/tmpU7WkCt/job_working_directory/000/10/galaxy.json /tmp/tmpU7WkCt/job_working_directory/000/10/metadata_in_HistoryDatasetAssociation_10_XxvsyL,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_kwds_HistoryDatasetAssociation_10_UkPyBp,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_out_HistoryDatasetAssociation_10_iHWDAF,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_results_HistoryDatasetAssociation_10_ajDjnM,,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_override_HistoryDatasetAssociation_10_luYSE7 /tmp/tmpU7WkCt/job_working_directory/000/10/metadata_in_HistoryDatasetAssociation_11_OLshpt,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_kwds_HistoryDatasetAssociation_11_MhTgjt,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_out_HistoryDatasetAssociation_11_ARDRmp,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_results_HistoryDatasetAssociation_11_YzIxny,,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_override_HistoryDatasetAssociation_11_uHS2xh /tmp/tmpU7WkCt/job_working_directory/000/10/metadata_in_HistoryDatasetAssociation_12_XPXisB,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_kwds_HistoryDatasetAssociation_12_xZeVXT,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_out_HistoryDatasetAssociation_12_pB_A6o,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_results_HistoryDatasetAssociation_12_e7v52k,,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_override_HistoryDatasetAssociation_12_zPVWk9 /tmp/tmpU7WkCt/job_working_directory/000/10/metadata_in_HistoryDatasetAssociation_13_knMr2v,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_kwds_HistoryDatasetAssociation_13_0otOpa,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_out_HistoryDatasetAssociation_13_8oTnho,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_results_HistoryDatasetAssociation_13_N0hjQB,,/tmp/tmpU7WkCt/job_working_directory/000/10/metadata_override_HistoryDatasetAssociation_13_SnpBxb; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (10) executing job script: /tmp/tmpU7WkCt/job_working_directory/000/10/galaxy_10.sh\ngalaxy.jobs: DEBUG: (10) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5449172d6ff5669b?key=d901781e67b8bb0595a0acef05cb2221 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/5449172d6ff5669b?key=d901781e67b8bb0595a0acef05cb2221 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/5449172d6ff5669b?key=d901781e67b8bb0595a0acef05cb2221 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/5449172d6ff5669b?key=d901781e67b8bb0595a0acef05cb2221 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/5449172d6ff5669b?key=d901781e67b8bb0595a0acef05cb2221 HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpU7WkCt/job_working_directory/000/10/galaxy_10.sh\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 10\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 11\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 12\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 13\ngalaxy.jobs: DEBUG: job 10 ended\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5449172d6ff5669b?key=d901781e67b8bb0595a0acef05cb2221 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/5449172d6ff5669b?full=true&key=d901781e67b8bb0595a0acef05cb2221 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/5449172d6ff5669b?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff/contents/b54fb481e575bccc/display?raw=true&key=d901781e67b8bb0595a0acef05cb2221 HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmpU7WkCt/jobfiles, ofn: /tmp/tmpU7WkCt/jobfiles/callpeak_control_part.bdg\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmpU7WkCt/jobfiles. saved /tmp/tmpU7WkCt/jobfiles/callpeak_control_part.bdg\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5449172d6ff5669b?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff/contents/80b8022ff3f677b7/display?raw=true&key=d901781e67b8bb0595a0acef05cb2221 HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmpU7WkCt/jobfiles, ofn: /tmp/tmpU7WkCt/jobfiles/callpeak_treatment_part.bdg\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmpU7WkCt/jobfiles. saved /tmp/tmpU7WkCt/jobfiles/callpeak_treatment_part.bdg\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5449172d6ff5669b?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff/contents/5449172d6ff5669b/display?raw=true&key=d901781e67b8bb0595a0acef05cb2221 HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmpU7WkCt/jobfiles, ofn: /tmp/tmpU7WkCt/jobfiles/callpeak_part.bed\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmpU7WkCt/jobfiles. saved /tmp/tmpU7WkCt/jobfiles/callpeak_part.bed\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5449172d6ff5669b?key=d901781e67b8bb0595a0acef05cb2221 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/8155e4b4bf1581ff/contents/9ce08b2254e4d5ed/display?raw=true&key=d901781e67b8bb0595a0acef05cb2221 HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmpU7WkCt/jobfiles, ofn: /tmp/tmpU7WkCt/jobfiles/callpeak_summits_part.bed\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmpU7WkCt/jobfiles. saved /tmp/tmpU7WkCt/jobfiles/callpeak_summits_part.bed\n--------------------- >> end captured logging << ---------------------\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_macs2_callpeak.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"effective_genome_size_options|gsize": "3300000000", "effective_genome_size_options|effective_genome_size_options_selector": "user_defined", "infile": {"src": "hda", "id": "1ae74d26531588b0"}, "keep_dup_options|keep_dup_options_selector": "auto", "pvalue": "1e-5"}, "job": {"inputs": {"infile": {"src": "hda", "id": "1ae74d26531588b0"}}, "update_time": "2015-02-18T15:46:19.520860", "tool_id": "macs2_filterdup", "outputs": {"outfile": {"src": "hda", "id": "440a6c2b5d9efe20"}}, "stdout": "", "command_line": "macs2 filterdup -i \"/tmp/tmpU7WkCtfiles/000/dataset_14.dat\" -o temp_outfile  --format 'BED'  --gsize \"3300000000\"    --pvalue \"1e-5\" --keep-dup \"auto\" ; mv temp_outfile \"/tmp/tmpU7WkCtfiles/000/dataset_15.dat\"", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T15:46:14.082277", "params": {"tsize": "\"-1.0\"", "effective_genome_size_options": "{\"gsize\": \"3300000000\", \"effective_genome_size_options_selector\": \"user_defined\", \"__current_case__\": 0}", "keep_dup_options": "{\"__current_case__\": 3, \"keep_dup_options_selector\": \"auto\"}", "dbkey": "\"hg17\"", "chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "pvalue": "\"1e-5\""}, "stderr": "INFO  @ Wed, 18 Feb 2015 10:46:16: read tag files... \nINFO  @ Wed, 18 Feb 2015 10:46:16: read alignment tags... \nINFO  @ Wed, 18 Feb 2015 10:46:16: tag size is determined as 100 bps \nINFO  @ Wed, 18 Feb 2015 10:46:16: tag size = 100 \nINFO  @ Wed, 18 Feb 2015 10:46:16:  total tags in alignment file: 13 \nINFO  @ Wed, 18 Feb 2015 10:46:16: calculate max duplicate tags in single position based on binomal distribution... \nINFO  @ Wed, 18 Feb 2015 10:46:16:  max_dup_tags based on binomal = 0 \nINFO  @ Wed, 18 Feb 2015 10:46:16: filter out redundant tags at the same location and the same strand by allowing at most 0 tag(s) \nINFO  @ Wed, 18 Feb 2015 10:46:16:  tags after filtering in alignment file: 10 \nINFO  @ Wed, 18 Feb 2015 10:46:16:  Redundant rate of alignment file: 0.23 \nINFO  @ Wed, 18 Feb 2015 10:46:16: Write to BED file \nINFO  @ Wed, 18 Feb 2015 10:46:16: finished! Check temp_outfile. \n", "job_metrics": [], "model_class": "Job", "external_id": "10467", "id": "80b8022ff3f677b7", "user_email": "[e-mail]"}}, "id": "functional.test_toolbox.TestForTool_macs2_filterdup.test_tool_000000", "has_data": true}, {"data": {"status": "failure", "inputs": {"mfoldlo": "5", "tsize": "-1.0", "effective_genome_size_options|gsize": "3300000000", "infiles": [{"src": "hda", "id": "ea0b941dfbe636f8"}, {"src": "hda", "id": "27ee89e2e3d631e0"}], "effective_genome_size_options|effective_genome_size_options_selector": "user_defined", "mfoldhi": "50", "band_width": "300"}, "output_problems": ["Files /tmp/tmpU7WkCt/tmp/tmpL9LasJpredictd_on_ChIP_200K_and_Control_200K.pdf=22595b but /var/lib/jenkins/workspace/TTS-Pusher/tools/macs2/test-data/predictd_on_ChIP_200K_and_Control_200K.pdf=65536b - compare (delta=10000) failed"], "job": {"inputs": {"infiles2": {"src": "hda", "id": "27ee89e2e3d631e0"}, "infiles": {"src": "hda", "id": "ea0b941dfbe636f8"}, "infiles1": {"src": "hda", "id": "ea0b941dfbe636f8"}}, "update_time": "2015-02-18T15:46:54.737261", "tool_id": "macs2_predictd", "outputs": {"outfile": {"src": "hda", "id": "61f03d5eef6f1538"}, "outfile_image": {"src": "hda", "id": "d5b3e51b7b790121"}}, "stdout": "null device \n          1 \n", "command_line": "macs2 predictd -i \"/tmp/tmpU7WkCtfiles/000/dataset_16.dat\" \"/tmp/tmpU7WkCtfiles/000/dataset_17.dat\"    --gsize \"3300000000\"  --bw \"300\" --mfold \"5\" \"50\"  2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'  > \"/tmp/tmpU7WkCtfiles/000/dataset_18.dat\"  &&  Rscript predictd", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T15:46:46.348865", "params": {"mfoldlo": "\"5\"", "tsize": "\"-1.0\"", "effective_genome_size_options": "{\"gsize\": \"3300000000\", \"effective_genome_size_options_selector\": \"user_defined\", \"__current_case__\": 0}", "dbkey": "\"hg17\"", "mfoldhi": "\"50\"", "chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "band_width": "\"300\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "10500", "id": "440a6c2b5d9efe20", "user_email": "[e-mail]"}, "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: Files /tmp/tmpU7WkCt/tmp/tmpL9LasJpredictd_on_ChIP_200K_and_Control_200K.pdf=22595b but /var/lib/jenkins/workspace/TTS-Pusher/tools/macs2/test-data/predictd_on_ChIP_200K_and_Control_200K.pdf=65536b - compare (delta=10000) failed\n-------------------- >> begin captured logging << --------------------\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/users?key=test_key HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nurllib3.connectionpool: DEBUG: Setting read timeout to None\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 13\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: (13) Working directory for job is: /tmp/tmpU7WkCt/job_working_directory/000/13\ngalaxy.jobs.handler: DEBUG: (13) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/histories/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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: (13) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (13) Job dispatched\nurllib3.connectionpool: DEBUG: \"GET /api/histories/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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: (13) command is: python /var/lib/jenkins/galaxy/default/tools/data_source/upload.py /var/lib/jenkins/galaxy/default /tmp/tmpU7WkCt/tmp/tmpJBkl_S /tmp/tmpU7WkCt/tmp/tmpSxiaBO 16:/tmp/tmpU7WkCt/job_working_directory/000/13/dataset_16_files:/tmp/tmpU7WkCtfiles/000/dataset_16.dat; return_code=$?; cd /var/lib/jenkins/galaxy/default; /var/lib/jenkins/galaxy/default/set_metadata.sh /tmp/tmpU7WkCtfiles /tmp/tmpU7WkCt/job_working_directory/000/13 . /tmp/tmpsnDH3q/functional_tests_wsgi.ini /tmp/tmpU7WkCt/tmp/tmpJBkl_S /tmp/tmpU7WkCt/job_working_directory/000/13/galaxy.json /tmp/tmpU7WkCt/job_working_directory/000/13/metadata_in_HistoryDatasetAssociation_16_umSeem,/tmp/tmpU7WkCt/job_working_directory/000/13/metadata_kwds_HistoryDatasetAssociation_16_U0dJov,/tmp/tmpU7WkCt/job_working_directory/000/13/metadata_out_HistoryDatasetAssociation_16_NxcNem,/tmp/tmpU7WkCt/job_working_directory/000/13/metadata_results_HistoryDatasetAssociation_16_2CTkuS,,/tmp/tmpU7WkCt/job_working_directory/000/13/metadata_override_HistoryDatasetAssociation_16_3oT6wJ; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (13) executing job script: /tmp/tmpU7WkCt/job_working_directory/000/13/galaxy_13.sh\ngalaxy.jobs: DEBUG: (13) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: DEBUG: \"GET /api/histories/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpU7WkCt/job_working_directory/000/13/galaxy_13.sh\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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 16\nurllib3.connectionpool: DEBUG: \"GET /api/histories/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: job 13 ended\nurllib3.connectionpool: DEBUG: Setting read timeout to None\ngalaxy.tools.actions.upload_common: INFO: tool upload1 created job id 14\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: (14) Working directory for job is: /tmp/tmpU7WkCt/job_working_directory/000/14\ngalaxy.jobs.handler: DEBUG: (14) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/histories/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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: (14) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (14) Job dispatched\nurllib3.connectionpool: DEBUG: \"GET /api/histories/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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: (14) command is: python /var/lib/jenkins/galaxy/default/tools/data_source/upload.py /var/lib/jenkins/galaxy/default /tmp/tmpU7WkCt/tmp/tmpJBkl_S /tmp/tmpU7WkCt/tmp/tmpWAWvII 17:/tmp/tmpU7WkCt/job_working_directory/000/14/dataset_17_files:/tmp/tmpU7WkCtfiles/000/dataset_17.dat; return_code=$?; cd /var/lib/jenkins/galaxy/default; /var/lib/jenkins/galaxy/default/set_metadata.sh /tmp/tmpU7WkCtfiles /tmp/tmpU7WkCt/job_working_directory/000/14 . /tmp/tmpsnDH3q/functional_tests_wsgi.ini /tmp/tmpU7WkCt/tmp/tmpJBkl_S /tmp/tmpU7WkCt/job_working_directory/000/14/galaxy.json /tmp/tmpU7WkCt/job_working_directory/000/14/metadata_in_HistoryDatasetAssociation_17_xpQAS2,/tmp/tmpU7WkCt/job_working_directory/000/14/metadata_kwds_HistoryDatasetAssociation_17_p9Rvno,/tmp/tmpU7WkCt/job_working_directory/000/14/metadata_out_HistoryDatasetAssociation_17_ifOtUK,/tmp/tmpU7WkCt/job_working_directory/000/14/metadata_results_HistoryDatasetAssociation_17_Vxvv_7,,/tmp/tmpU7WkCt/job_working_directory/000/14/metadata_override_HistoryDatasetAssociation_17_SVUHog; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (14) executing job script: /tmp/tmpU7WkCt/job_working_directory/000/14/galaxy_14.sh\nurllib3.connectionpool: DEBUG: \"GET /api/histories/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: (14) Persisting job destination (destination id: local:///)\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpU7WkCt/job_working_directory/000/14/galaxy_14.sh\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/histories/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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 17\nurllib3.connectionpool: DEBUG: \"GET /api/histories/fa6d20d0fb68383f?key=e15f0258a955e753a089c754ea3086fd 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 14 ended\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: (15) Working directory for job is: /tmp/tmpU7WkCt/job_working_directory/000/15\ngalaxy.jobs.handler: DEBUG: (15) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/440a6c2b5d9efe20?key=e15f0258a955e753a089c754ea3086fd HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: (15) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (15) 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/440a6c2b5d9efe20?key=e15f0258a955e753a089c754ea3086fd 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: (15) command is: macs2 --version > /tmp/tmpU7WkCt/tmp/GALAXY_VERSION_STRING_15 2>&1; macs2 predictd -i \"/tmp/tmpU7WkCtfiles/000/dataset_16.dat\" \"/tmp/tmpU7WkCtfiles/000/dataset_17.dat\"    --gsize \"3300000000\"  --bw \"300\" --mfold \"5\" \"50\"  2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'  > \"/tmp/tmpU7WkCtfiles/000/dataset_18.dat\"  &&  Rscript predictd; return_code=$?; if [ -f /tmp/tmpU7WkCt/job_working_directory/000/15/predictd_model.pdf ] ; then cp /tmp/tmpU7WkCt/job_working_directory/000/15/predictd_model.pdf /tmp/tmpU7WkCtfiles/000/dataset_19.dat ; fi; cd /var/lib/jenkins/galaxy/default; /var/lib/jenkins/galaxy/default/set_metadata.sh /tmp/tmpU7WkCtfiles /tmp/tmpU7WkCt/job_working_directory/000/15 . /tmp/tmpsnDH3q/functional_tests_wsgi.ini /tmp/tmpU7WkCt/tmp/tmpJBkl_S /tmp/tmpU7WkCt/job_working_directory/000/15/galaxy.json /tmp/tmpU7WkCt/job_working_directory/000/15/metadata_in_HistoryDatasetAssociation_18_dHc851,/tmp/tmpU7WkCt/job_working_directory/000/15/metadata_kwds_HistoryDatasetAssociation_18_GbjX2E,/tmp/tmpU7WkCt/job_working_directory/000/15/metadata_out_HistoryDatasetAssociation_18_csL_cU,/tmp/tmpU7WkCt/job_working_directory/000/15/metadata_results_HistoryDatasetAssociation_18_DftZH0,,/tmp/tmpU7WkCt/job_working_directory/000/15/metadata_override_HistoryDatasetAssociation_18_LVvlfX /tmp/tmpU7WkCt/job_working_directory/000/15/metadata_in_HistoryDatasetAssociation_19_oegLQZ,/tmp/tmpU7WkCt/job_working_directory/000/15/metadata_kwds_HistoryDatasetAssociation_19_TwykAs,/tmp/tmpU7WkCt/job_working_directory/000/15/metadata_out_HistoryDatasetAssociation_19_S9Mntv,/tmp/tmpU7WkCt/job_working_directory/000/15/metadata_results_HistoryDatasetAssociation_19_6tX9eo,,/tmp/tmpU7WkCt/job_working_directory/000/15/metadata_override_HistoryDatasetAssociation_19_L8wGS0; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (15) executing job script: /tmp/tmpU7WkCt/job_working_directory/000/15/galaxy_15.sh\ngalaxy.jobs: DEBUG: (15) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/440a6c2b5d9efe20?key=e15f0258a955e753a089c754ea3086fd HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpU7WkCt/job_working_directory/000/15/galaxy_15.sh\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 18\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 19\ngalaxy.jobs: DEBUG: job 15 ended\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/440a6c2b5d9efe20?key=e15f0258a955e753a089c754ea3086fd 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/440a6c2b5d9efe20?full=true&key=e15f0258a955e753a089c754ea3086fd 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/440a6c2b5d9efe20?key=e15f0258a955e753a089c754ea3086fd 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/fa6d20d0fb68383f/contents/61f03d5eef6f1538/display?raw=true&key=e15f0258a955e753a089c754ea3086fd HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmpU7WkCt/jobfiles, ofn: /tmp/tmpU7WkCt/jobfiles/predictd_on_ChIP_200K_and_Control_200K.txt\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmpU7WkCt/jobfiles. saved /tmp/tmpU7WkCt/jobfiles/predictd_on_ChIP_200K_and_Control_200K.txt\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: Setting read timeout to None\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/440a6c2b5d9efe20?key=e15f0258a955e753a089c754ea3086fd 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/fa6d20d0fb68383f/contents/d5b3e51b7b790121/display?raw=true&key=e15f0258a955e753a089c754ea3086fd HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmpU7WkCt/jobfiles, ofn: /tmp/tmpU7WkCt/jobfiles/predictd_on_ChIP_200K_and_Control_200K.pdf\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmpU7WkCt/jobfiles. saved /tmp/tmpU7WkCt/jobfiles/predictd_on_ChIP_200K_and_Control_200K.pdf\n--------------------- >> end captured logging << ---------------------\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_macs2_predictd.test_tool_000000", "has_data": true}, {"data": {"status": "success", "inputs": {"bed_infile": {"src": "hda", "id": "c18708cec3343c17"}, "winsize": "200", "infile": {"src": "hda", "id": "b28067233c6d9fa0"}, "cutoff": "5.0"}, "job": {"inputs": {"bed_infile": {"src": "hda", "id": "c18708cec3343c17"}, "infile": {"src": "hda", "id": "b28067233c6d9fa0"}}, "update_time": "2015-02-18T15:47:30.751931", "tool_id": "macs2_refinepeak", "outputs": {"outfile": {"src": "hda", "id": "5ca39fba41b940d1"}}, "stdout": "", "command_line": "macs2 refinepeak -b \"/tmp/tmpU7WkCtfiles/000/dataset_21.dat\" -i \"/tmp/tmpU7WkCtfiles/000/dataset_20.dat\" --format 'BED' --cutoff \"5.0\" --window-size \"200\" --ofile \"/tmp/tmpU7WkCtfiles/000/dataset_22.dat\"", "exit_code": 0, "state": "ok", "create_time": "2015-02-18T15:47:23.545195", "params": {"cutoff": "\"5.0\"", "winsize": "\"200\"", "chromInfo": "\"/var/lib/jenkins/galaxy/default/tool-data/shared/ucsc/chrom/hg17.len\"", "dbkey": "\"hg17\""}, "stderr": "INFO  @ Wed, 18 Feb 2015 10:47:27: read tag files... \nINFO  @ Wed, 18 Feb 2015 10:47:27: read alignment tags... \nINFO  @ Wed, 18 Feb 2015 10:47:27: tag size is determined as 100 bps \nINFO  @ Wed, 18 Feb 2015 10:47:28: Done! \nINFO  @ Wed, 18 Feb 2015 10:47:28: Check output file: /tmp/tmpU7WkCtfiles/000/dataset_22.dat_refinepeak.bed \n", "job_metrics": [], "model_class": "Job", "external_id": "10545", "id": "61f03d5eef6f1538", "user_email": "[e-mail]"}}, "id": "functional.test_toolbox.TestForTool_macs2_refinepeak.test_tool_000000", "has_data": true}], "version": "0.1", "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 2, "num_tests": 7}}