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{"tests": [{"data": {"status": "failure", "inputs": {"advancedOpt|showAdvancedOpt": "no", "bigwigFile2": {"src": "hda", "id": "2891970512fa2d5a"}, "comparison|comparison_select": "ratio", "outFileFormat": "bigwig", "bigwigFile1": {"src": "hda", "id": "2891970512fa2d5a"}}, "output_problems": ["Job in error state.", "Job in error state."], "job": {"inputs": {"bigwigFile2": {"src": "hda", "id": "2891970512fa2d5a"}, "bigwigFile1": {"src": "hda", "id": "2891970512fa2d5a"}}, "update_time": "2015-01-21T14:00:16.502455", "tool_id": "deeptools_bigwigCompare", "outputs": {"outFileName": {"src": "hda", "id": "5729865256bc2525"}}, "stdout": "", "command_line": "bigwigCompare  --numberOfProcessors \"${GALAXY_SLOTS:-4}\"  --bigwig1 '/tmp/tmpPIgGHsfiles/000/dataset_1.dat' --bigwig2 '/tmp/tmpPIgGHsfiles/000/dataset_1.dat'  --outFileName '/tmp/tmpPIgGHsfiles/000/dataset_2.dat' --outFileFormat 'bigwig'  --ratio ratio  --pseudocount 1.0", "exit_code": 1, "state": "error", "create_time": "2015-01-21T14:00:03.956345", "params": {"comparison": "{\"pseudocount\": \"1.0\", \"__current_case__\": 1, \"comparison_select\": \"ratio\"}", "outFileFormat": "\"bigwig\"", "region": "\"\"", "dbkey": "\"hg17\"", "advancedOpt": "{\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}", "chromInfo": "\"/home/bag/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "Fatal error: Exit code 1 ()\n\n######################################################\n\nThe program *bedGraphToBigWig* was not found in your PATH. In\norder for deeptools to work properly this program needs\nto be installed. If you already have a copy of this\nprogram please be sure that it is found in your PATH or\nthat is referred in the configuration file of deepTools\nlocated at:\n\n/home/bag/.local/lib/python2.7/site-packages/deeptools/config/deeptools.cfg\n\nThe program can be downloaded from here:\n  http://hgdownload.cse.ucsc.edu/admin/exe/\n\n\n########################################################\n\nThe output is set by default to 'bedgraph'\nsh: 1: bigWigInfo: not found\nsh: 1: bigWigInfo: not found\nError: The generated bedGraphFile was empty. Please adjust\nyour deepTools settings and check your input files.", "job_metrics": [], "model_class": "Job", "external_id": "17230", "id": "5729865256bc2525", "user_email": "[e-mail]"}, "problem_log": "Traceback (most recent call last):\n  File \"/usr/lib/python2.7/unittest/case.py\", line 329, in run\n    testMethod()\n  File \"/home/bag/projects/code/galaxy-central/test/functional/test_toolbox.py\", line 223, in test_tool\n    self.do_it( td )\n  File \"/home/bag/projects/code/galaxy-central/test/functional/test_toolbox.py\", line 66, in do_it\n    raise e\nJobOutputsError: Job in error state.\nJob in error state.\n-------------------- >> begin captured stdout << ---------------------\nHistory with id 2891970512fa2d5a in error - summary of datasets in error below.\n--------------------------------------\n| 2 - bigwigCompare on data 1 (HID - NAME) \n| Dataset Blurb:\n|  error\n| Dataset Info:\n|  Fatal error: Exit code 1 ()\n|  ######################################################\n|  The program *bedGraphToBigWig* was not found in your PATH. In\n|  order for deeptools to work properly this program needs\n|  to be installed. If you already have a copy of this\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  Fatal error: Exit code 1 ()\n|  ######################################################\n|  The program *bedGraphToBigWig* was not found in your PATH. In\n|  order for deeptools to work properly this program needs\n|  to be installed. If you already have a copy of this\n|  program please be sure that it is found in your PATH or\n|  that is referred in the configuration file of deepTools\n|  located at:\n|  /home/bag/.local/lib/python2.7/site-packages/deeptools/config/deeptools.cfg\n|  The program can be downloaded from here:\n|  http://hgdownload.cse.ucsc.edu/admin/exe/\n|  ########################################################\n|  The output is set by default to 'bedgraph'\n|  sh: 1: bigWigInfo: not found\n|  sh: 1: bigWigInfo: not found\n|  Error: The generated bedGraphFile was empty. Please adjust\n|  your deepTools settings and check your input files.\n|\n--------------------------------------\nHistory with id 2891970512fa2d5a in error - summary of datasets in error below.\n--------------------------------------\n| 2 - bigwigCompare on data 1 (HID - NAME) \n| Dataset Blurb:\n|  error\n| Dataset Info:\n|  Fatal error: Exit code 1 ()\n|  ######################################################\n|  The program *bedGraphToBigWig* was not found in your PATH. In\n|  order for deeptools to work properly this program needs\n|  to be installed. If you already have a copy of this\n| Dataset Job Standard Output:\n|  *Standard output was empty.*\n| Dataset Job Standard Error:\n|  Fatal error: Exit code 1 ()\n|  ######################################################\n|  The program *bedGraphToBigWig* was not found in your PATH. In\n|  order for deeptools to work properly this program needs\n|  to be installed. If you already have a copy of this\n|  program please be sure that it is found in your PATH or\n|  that is referred in the configuration file of deepTools\n|  located at:\n|  /home/bag/.local/lib/python2.7/site-packages/deeptools/config/deeptools.cfg\n|  The program can be downloaded from here:\n|  http://hgdownload.cse.ucsc.edu/admin/exe/\n|  ########################################################\n|  The output is set by default to 'bedgraph'\n|  sh: 1: bigWigInfo: not found\n|  sh: 1: bigWigInfo: not found\n|  Error: The generated bedGraphFile was empty. Please adjust\n|  your deepTools settings and check your input files.\n|\n--------------------------------------\n\n--------------------- >> end captured stdout << ----------------------\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: \"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: \"POST /api/users 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: \"POST /api/users/2891970512fa2d5a/api_key HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"POST /api/histories HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\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\ngalaxy.jobs: DEBUG: (1) Working directory for job is: /tmp/tmpPIgGHs/job_working_directory/000/1\ngalaxy.jobs.handler: DEBUG: (1) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\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 /home/bag/projects/code/galaxy-central/tools/data_source/upload.py /home/bag/projects/code/galaxy-central /tmp/tmpPIgGHs/tmp/tmp0PJepF /tmp/tmpPIgGHs/tmp/tmpRpbhPM 1:/tmp/tmpPIgGHs/job_working_directory/000/1/dataset_1_files:/tmp/tmpPIgGHsfiles/000/dataset_1.dat; return_code=$?; cd /home/bag/projects/code/galaxy-central; /home/bag/projects/code/galaxy-central/set_metadata.sh /tmp/tmpPIgGHsfiles /tmp/tmpPIgGHs/job_working_directory/000/1 . /tmp/tmpv0gVHj/functional_tests_wsgi.ini /tmp/tmpPIgGHs/tmp/tmp0PJepF /tmp/tmpPIgGHs/job_working_directory/000/1/galaxy.json /tmp/tmpPIgGHs/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_ccsVhS,/tmp/tmpPIgGHs/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_Qq5BwN,/tmp/tmpPIgGHs/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_WKo1fr,/tmp/tmpPIgGHs/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_cB8OGx,,/tmp/tmpPIgGHs/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_hOnJAL; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/tmpPIgGHs/job_working_directory/000/1/galaxy_1.sh\ngalaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpPIgGHs/job_working_directory/000/1/galaxy_1.sh\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 1\ngalaxy.jobs: DEBUG: job 1 ended\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/tmpPIgGHs/job_working_directory/000/2\ngalaxy.jobs.handler: DEBUG: (2) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.handler: INFO: (2) Job dispatched\ngalaxy.jobs.runners: DEBUG: (2) command is: bigwigCompare --version > /tmp/tmpPIgGHs/tmp/GALAXY_VERSION_STRING_2 2>&1; bigwigCompare  --numberOfProcessors \"${GALAXY_SLOTS:-4}\"  --bigwig1 '/tmp/tmpPIgGHsfiles/000/dataset_1.dat' --bigwig2 '/tmp/tmpPIgGHsfiles/000/dataset_1.dat'  --outFileName '/tmp/tmpPIgGHsfiles/000/dataset_2.dat' --outFileFormat 'bigwig'  --ratio ratio  --pseudocount 1.0; return_code=$?; cd /home/bag/projects/code/galaxy-central; /home/bag/projects/code/galaxy-central/set_metadata.sh /tmp/tmpPIgGHsfiles /tmp/tmpPIgGHs/job_working_directory/000/2 . /tmp/tmpv0gVHj/functional_tests_wsgi.ini /tmp/tmpPIgGHs/tmp/tmp0PJepF /tmp/tmpPIgGHs/job_working_directory/000/2/galaxy.json /tmp/tmpPIgGHs/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_rw8GcL,/tmp/tmpPIgGHs/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_hap93L,/tmp/tmpPIgGHs/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_fGfc3v,/tmp/tmpPIgGHs/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_IUTLzd,,/tmp/tmpPIgGHs/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_BgsayE; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/tmpPIgGHs/job_working_directory/000/2/galaxy_2.sh\ngalaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpPIgGHs/job_working_directory/000/2/galaxy_2.sh\ngalaxy.jobs.output_checker: INFO: Job 2: Fatal error: Exit code 1 ()\ngalaxy.jobs: DEBUG: setting dataset state to ERROR\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: job 2 ended\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?full=true&key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=794abbf3a83634a1b1a8f47086cf5714 HTTP/1.1\" 200 None\n--------------------- >> end captured logging << ---------------------\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_deeptools_bigwigCompare.test_tool_000000", "has_data": true}, {"data": {"status": "failure", "inputs": {"advancedOpt|showAdvancedOpt": "no", "bigwigFile2": {"src": "hda", "id": "54f2a3a23292eb07"}, "comparison|comparison_select": "ratio", "outFileFormat": "bedgraph", "bigwigFile1": {"src": "hda", "id": "54f2a3a23292eb07"}}, "output_problems": ["History item  different than expected, difference (using diff):\n( /home/bag/projects/code/deepTools/galaxy/wrapper/test-data/bigwigCompare_result2.bg v. /tmp/tmpPIgGHs/tmp/tmpGqBqc9bigwigCompare_result2.bg )\n--- local_file\n+++ history_data\n@@ -1,5 +0,0 @@\n-chr21\t0\t10000000\t1.0\n-chr21\t10000000\t20000000\t1.0\n-chr21\t20000000\t30000000\t1.0\n-chr21\t30000000\t40000000\t1.0\n-chr21\t40000000\t48129895\t1.0\n"], "job": {"inputs": {"bigwigFile2": {"src": "hda", "id": "54f2a3a23292eb07"}, "bigwigFile1": {"src": "hda", "id": "54f2a3a23292eb07"}}, "update_time": "2015-01-21T14:00:46.256358", "tool_id": "deeptools_bigwigCompare", "outputs": {"outFileName": {"src": "hda", "id": "8155e4b4bf1581ff"}}, "stdout": "", "command_line": "bigwigCompare  --numberOfProcessors \"${GALAXY_SLOTS:-4}\"  --bigwig1 '/tmp/tmpPIgGHsfiles/000/dataset_3.dat' --bigwig2 '/tmp/tmpPIgGHsfiles/000/dataset_3.dat'  --outFileName '/tmp/tmpPIgGHsfiles/000/dataset_4.dat' --outFileFormat 'bedgraph'  --ratio ratio  --pseudocount 1.0", "exit_code": 0, "state": "ok", "create_time": "2015-01-21T14:00:37.272522", "params": {"comparison": "{\"pseudocount\": \"1.0\", \"__current_case__\": 1, \"comparison_select\": \"ratio\"}", "outFileFormat": "\"bedgraph\"", "region": "\"\"", "dbkey": "\"hg17\"", "advancedOpt": "{\"showAdvancedOpt\": \"no\", \"__current_case__\": 0}", "chromInfo": "\"/home/bag/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/hg17.len\""}, "stderr": "\n######################################################\n\nThe program *bedGraphToBigWig* was not found in your PATH. In\norder for deeptools to work properly this program needs\nto be installed. If you already have a copy of this\nprogram please be sure that it is found in your PATH or\nthat is referred in the configuration file of deepTools\nlocated at:\n\n/home/bag/.local/lib/python2.7/site-packages/deeptools/config/deeptools.cfg\n\nThe program can be downloaded from here:\n  http://hgdownload.cse.ucsc.edu/admin/exe/\n\n\n########################################################\n\nThe output is set by default to 'bedgraph'\nsh: 1: bigWigInfo: not found\nsh: 1: bigWigInfo: not found\n", "job_metrics": [], "model_class": "Job", "external_id": "17321", "id": "8155e4b4bf1581ff", "user_email": "[e-mail]"}, "problem_log": "Traceback (most recent call last):\n  File \"/usr/lib/python2.7/unittest/case.py\", line 329, in run\n    testMethod()\n  File \"/home/bag/projects/code/galaxy-central/test/functional/test_toolbox.py\", line 223, in test_tool\n    self.do_it( td )\n  File \"/home/bag/projects/code/galaxy-central/test/functional/test_toolbox.py\", line 66, in do_it\n    raise e\nJobOutputsError: History item  different than expected, difference (using diff):\n( /home/bag/projects/code/deepTools/galaxy/wrapper/test-data/bigwigCompare_result2.bg v. /tmp/tmpPIgGHs/tmp/tmpGqBqc9bigwigCompare_result2.bg )\n--- local_file\n+++ history_data\n@@ -1,5 +0,0 @@\n-chr21\t0\t10000000\t1.0\n-chr21\t10000000\t20000000\t1.0\n-chr21\t20000000\t30000000\t1.0\n-chr21\t30000000\t40000000\t1.0\n-chr21\t40000000\t48129895\t1.0\n\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: \"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: \"POST /api/users/2891970512fa2d5a/api_key HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"POST /api/histories HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.tools.actions.upload_common: INFO: tool upload1 created job id 3\nurllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (3) Working directory for job is: /tmp/tmpPIgGHs/job_working_directory/000/3\ngalaxy.jobs.handler: DEBUG: (3) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (3) Job dispatched\nurllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.runners: DEBUG: (3) command is: python /home/bag/projects/code/galaxy-central/tools/data_source/upload.py /home/bag/projects/code/galaxy-central /tmp/tmpPIgGHs/tmp/tmp0PJepF /tmp/tmpPIgGHs/tmp/tmpz8wZrv 3:/tmp/tmpPIgGHs/job_working_directory/000/3/dataset_3_files:/tmp/tmpPIgGHsfiles/000/dataset_3.dat; return_code=$?; cd /home/bag/projects/code/galaxy-central; /home/bag/projects/code/galaxy-central/set_metadata.sh /tmp/tmpPIgGHsfiles /tmp/tmpPIgGHs/job_working_directory/000/3 . /tmp/tmpv0gVHj/functional_tests_wsgi.ini /tmp/tmpPIgGHs/tmp/tmp0PJepF /tmp/tmpPIgGHs/job_working_directory/000/3/galaxy.json /tmp/tmpPIgGHs/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_3_M641RK,/tmp/tmpPIgGHs/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_vknCha,/tmp/tmpPIgGHs/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_3_RHHbx7,/tmp/tmpPIgGHs/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_3_Scjshu,,/tmp/tmpPIgGHs/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_3_B79aAL; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (3) executing job script: /tmp/tmpPIgGHs/job_working_directory/000/3/galaxy_3.sh\ngalaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpPIgGHs/job_working_directory/000/3/galaxy_3.sh\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 3\ngalaxy.jobs: DEBUG: job 3 ended\nurllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (4) Working directory for job is: /tmp/tmpPIgGHs/job_working_directory/000/4\ngalaxy.jobs.handler: DEBUG: (4) Dispatching to local runner\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/8155e4b4bf1581ff?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (4) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (4) Job dispatched\ngalaxy.jobs.runners: DEBUG: (4) command is: bigwigCompare --version > /tmp/tmpPIgGHs/tmp/GALAXY_VERSION_STRING_4 2>&1; bigwigCompare  --numberOfProcessors \"${GALAXY_SLOTS:-4}\"  --bigwig1 '/tmp/tmpPIgGHsfiles/000/dataset_3.dat' --bigwig2 '/tmp/tmpPIgGHsfiles/000/dataset_3.dat'  --outFileName '/tmp/tmpPIgGHsfiles/000/dataset_4.dat' --outFileFormat 'bedgraph'  --ratio ratio  --pseudocount 1.0; return_code=$?; cd /home/bag/projects/code/galaxy-central; /home/bag/projects/code/galaxy-central/set_metadata.sh /tmp/tmpPIgGHsfiles /tmp/tmpPIgGHs/job_working_directory/000/4 . /tmp/tmpv0gVHj/functional_tests_wsgi.ini /tmp/tmpPIgGHs/tmp/tmp0PJepF /tmp/tmpPIgGHs/job_working_directory/000/4/galaxy.json /tmp/tmpPIgGHs/job_working_directory/000/4/metadata_in_HistoryDatasetAssociation_4_ZCW55i,/tmp/tmpPIgGHs/job_working_directory/000/4/metadata_kwds_HistoryDatasetAssociation_4_HKOLTz,/tmp/tmpPIgGHs/job_working_directory/000/4/metadata_out_HistoryDatasetAssociation_4_aEOFWP,/tmp/tmpPIgGHs/job_working_directory/000/4/metadata_results_HistoryDatasetAssociation_4_O_YvpP,,/tmp/tmpPIgGHs/job_working_directory/000/4/metadata_override_HistoryDatasetAssociation_4_KJj66T; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (4) executing job script: /tmp/tmpPIgGHs/job_working_directory/000/4/galaxy_4.sh\ngalaxy.jobs: DEBUG: (4) Persisting job destination (destination id: local:///)\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/8155e4b4bf1581ff?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpPIgGHs/job_working_directory/000/4/galaxy_4.sh\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/8155e4b4bf1581ff?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: job 4 ended\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/8155e4b4bf1581ff?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/8155e4b4bf1581ff?full=true&key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/jobs/8155e4b4bf1581ff?key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nurllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nurllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525/contents/8155e4b4bf1581ff/display?raw=true&key=ebf1bf74e329708d41af422e0d7efc0e HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmpPIgGHs/jobfiles, ofn: /tmp/tmpPIgGHs/jobfiles/bigwigCompare_result2.bg\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmpPIgGHs/jobfiles. saved /tmp/tmpPIgGHs/jobfiles/bigwigCompare_result2.bg\nbase.twilltestcase: INFO: ## files diff on /home/bag/projects/code/deepTools/galaxy/wrapper/test-data/bigwigCompare_result2.bg and /tmp/tmpPIgGHs/tmp/tmpGqBqc9bigwigCompare_result2.bg lines_diff=0, found diff = 5\n--------------------- >> end captured logging << ---------------------\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_deeptools_bigwigCompare.test_tool_000001", "has_data": true}], "version": "0.1", "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 2, "num_tests": 2}}