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date Wed, 22 Apr 2015 10:29:35 -0400
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    <title>Tool Test Results (powered by Planemo)</title>

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        var test_data = {"tests": [{"data": {"status": "failure", "inputs": {"use_reference|reference_source|ref_file": {"src": "hda", "id": "5729865256bc2525"}, "use_reference|reference_source|reference_source_selector": "history", "use_reference|use_ref_selector": "yes", "input_file": {"src": "hda", "id": "2891970512fa2d5a"}}, "output_problems": ["History item  different than expected, difference (using diff):\n( /Users/marten/devel/git/tools-devteam/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out1.tab v. /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpVPmlQNsamtools_stats_out1.tab )\n--- local_file\n+++ history_data\n@@ -1,5 +1,5 @@\n-# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats\n-# The command line was:  stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat\n+# This file was produced by samtools stats (1.2+htslib-1.2) and can be plotted using plot-bamstats\n+# The command line was:  stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_2.dat /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_1.dat\n # CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n CHK\t1bd20fd8\t58ad2167\t29883386\n"], "job": {"inputs": {"ref_file": {"src": "hda", "id": "5729865256bc2525"}, "input_file": {"src": "hda", "id": "2891970512fa2d5a"}}, "update_time": "2015-04-21T21:45:40.695226", "tool_id": "samtools_stats", "outputs": {"output": {"src": "hda", "id": "54f2a3a23292eb07"}}, "stdout": "", "command_line": "ln -s \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_2.dat\" && samtools faidx `basename \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_2.dat\"` && samtools stats \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_1.dat\" --coverage 1,1000,1  --GC-depth 20000.0 --insert-size 8000    --most-inserts 0.99 --trim-quality 0 --ref-seq \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_2.dat\" > \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_3.dat\"", "exit_code": 0, "state": "ok", "create_time": "2015-04-21T21:45:29.298433", "params": {"coverage_max": "\"1000\"", "gc_depth": "\"20000.0\"", "insert_size": "\"8000\"", "most_inserts": "\"0.99\"", "coverage_step": "\"1\"", "dbkey": "\"hg17\"", "coverage_min": "\"1\"", "read_length": "\"0\"", "trim_quality": "\"0\"", "filter_by_flags": "{\"filter_flags\": \"nofilter\", \"__current_case__\": 1}", "split_output": "{\"split_output_selector\": \"no\", \"__current_case__\": 0}", "use_reference": "{\"reference_source\": {\"ref_file\": 2, \"reference_source_selector\": \"history\", \"__current_case__\": 1}, \"use_ref_selector\": \"yes\", \"__current_case__\": 0}", "chromInfo": "\"/Users/marten/devel/git/galaxy/tool-data/shared/ucsc/chrom/hg17.len\"", "remove_dups": "\"False\""}, "stderr": "[fai_load] build FASTA index.\n", "job_metrics": [], "model_class": "Job", "external_id": "64545", "id": "54f2a3a23292eb07", "user_email": "test@bx.psu.edu"}, "problem_log": "Traceback (most recent call last):\n  File \"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/case.py\", line 331, in run\n    testMethod()\n  File \"/Users/marten/devel/git/galaxy/test/functional/test_toolbox.py\", line 268, in test_tool\n    self.do_it( td )\n  File \"/Users/marten/devel/git/galaxy/test/functional/test_toolbox.py\", line 67, in do_it\n    raise e\nJobOutputsError: History item  different than expected, difference (using diff):\n( /Users/marten/devel/git/tools-devteam/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out1.tab v. /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpVPmlQNsamtools_stats_out1.tab )\n--- local_file\n+++ history_data\n@@ -1,5 +1,5 @@\n-# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats\n-# The command line was:  stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat\n+# This file was produced by samtools stats (1.2+htslib-1.2) and can be plotted using plot-bamstats\n+# The command line was:  stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_2.dat /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_1.dat\n # CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n CHK\t1bd20fd8\t58ad2167\t29883386\n\n-------------------- >> begin captured logging << --------------------\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/users?key=test_key HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/users HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/users/2891970512fa2d5a/api_key HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/histories HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1\ngalaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (721.369 ms)\ngalaxy.jobs: DEBUG: (1) Working directory for job is: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/1\ngalaxy.jobs.handler: DEBUG: (1) Dispatching to local runner\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)\ngalaxy.jobs.runners: DEBUG: Job [1] queued (3701.848 ms)\ngalaxy.jobs.handler: INFO: (1) Job dispatched\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.runners: DEBUG: (1) command is: python /Users/marten/devel/git/galaxy/tools/data_source/upload.py /Users/marten/devel/git/galaxy /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpcOV73W /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpzTLxF3 1:/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/1/dataset_1_files:/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_1.dat; return_code=$?; python /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/1/set_metadata_aC_Epn.py /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpcOV73W /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/1/galaxy.json /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_2YHWg0,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_xxSWvK,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_gpHI_B,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_bOBqlz,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_1.dat,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_chT4qY; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (1) executing job script: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/1/galaxy_1.sh\ngalaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/1/galaxy_1.sh\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: job 1 ended (finish() executed in (3319.682 ms))\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.tools.actions.upload_common: INFO: tool upload1 created job id 2\ngalaxy.tools.execute: DEBUG: Tool [upload1] created job [2] (1436.682 ms)\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (2) Working directory for job is: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/2\ngalaxy.jobs.handler: DEBUG: (2) Dispatching to local runner\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)\ngalaxy.jobs.runners: DEBUG: Job [2] queued (2933.918 ms)\ngalaxy.jobs.handler: INFO: (2) Job dispatched\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.runners: DEBUG: (2) command is: python /Users/marten/devel/git/galaxy/tools/data_source/upload.py /Users/marten/devel/git/galaxy /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpcOV73W /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpQj7Vtj 2:/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/2/dataset_2_files:/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_2.dat; return_code=$?; python /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/2/set_metadata_EnSKJC.py /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpcOV73W /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/2/galaxy.json /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_EbkTIH,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_A_ZJxl,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_rYAxQD,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_1V3qgk,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_2.dat,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_LI0aVu; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (2) executing job script: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/2/galaxy_2.sh\ngalaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.runners.local: DEBUG: execution finished: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/2/galaxy_2.sh\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: job 2 ended (finish() executed in (5509.688 ms))\ngalaxy.tools.actions: INFO: Handled output (77.015 ms)\ngalaxy.tools.actions: INFO: Verified access to datasets (55.049 ms)\ngalaxy.tools.execute: DEBUG: Tool [samtools_stats] created job [3] (665.725 ms)\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: (3) Working directory for job is: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/3\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.handler: DEBUG: (3) Dispatching to local runner\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///)\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.runners: DEBUG: Job [3] queued (1882.584 ms)\ngalaxy.jobs.handler: INFO: (3) Job dispatched\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\ngalaxy.jobs.runners: DEBUG: (3) command is: samtools --version | head -n 1 | awk '{ print $2 }' > /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/GALAXY_VERSION_STRING_3 2>&1; ln -s \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_2.dat\" && samtools faidx `basename \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_2.dat\"` && samtools stats \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_1.dat\" --coverage 1,1000,1  --GC-depth 20000.0 --insert-size 8000    --most-inserts 0.99 --trim-quality 0 --ref-seq \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_2.dat\" > \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_3.dat\"; return_code=$?; python /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/3/set_metadata_Zey9XK.py /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpcOV73W /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/3/galaxy.json /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_3_c241v6,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_TUAqpX,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_3_fh3HTD,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_3_y4t5DA,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_3.dat,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_3_3rhcZs; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (3) executing job script: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/3/galaxy_3.sh\ngalaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///)\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/3/galaxy_3.sh\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: job 3 ended (finish() executed in (2080.708 ms))\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?full=true&key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/54f2a3a23292eb07?key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/display?raw=true&key=9b3be0c093fde28daf0ffc1ec9b125ca HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/jobfiles, ofn: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/jobfiles/samtools_stats_out1.tab\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/jobfiles. saved /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/jobfiles/samtools_stats_out1.tab\nbase.twilltestcase: INFO: ## files diff on /Users/marten/devel/git/tools-devteam/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out1.tab and /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpVPmlQNsamtools_stats_out1.tab lines_diff=2, found diff = 4\n--------------------- >> end captured logging << ---------------------\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_samtools_stats.test_tool_000000", "has_data": true}, {"data": {"status": "failure", "inputs": {"use_reference|reference_source|reference_source_selector": "history", "input_file": {"src": "hda", "id": "8155e4b4bf1581ff"}, "split_output|split_output_selector": "yes", "split_output|generate_tables": ["sn", "mpc", "gcc"], "use_reference|use_ref_selector": "yes", "use_reference|reference_source|ref_file": {"src": "hda", "id": "7b55dbb89df8f4e5"}}, "output_problems": ["History item  different than expected, difference (using diff):\n( /Users/marten/devel/git/tools-devteam/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2.tab v. /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpYr1M8Csamtools_stats_out2.tab )\n--- local_file\n+++ history_data\n@@ -1,5 +1,5 @@\n-# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats\n-# The command line was:  stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat\n+# This file was produced by samtools stats (1.2+htslib-1.2) and can be plotted using plot-bamstats\n+# The command line was:  stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_5.dat /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_4.dat\n # CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n CHK\t1bd20fd8\t58ad2167\t29883386\n"], "job": {"inputs": {"ref_file": {"src": "hda", "id": "7b55dbb89df8f4e5"}, "input_file": {"src": "hda", "id": "8155e4b4bf1581ff"}}, "update_time": "2015-04-21T21:46:44.081337", "tool_id": "samtools_stats", "outputs": {"__new_primary_file_output|Mismatches per cycle__": {"src": "hda", "id": "a90a30fafe298e1e"}, "__new_primary_file_output|Summary numbers__": {"src": "hda", "id": "b842d972534ccb3e"}, "__new_primary_file_output|ACGT content per cycle__": {"src": "hda", "id": "683bc220e21425bb"}, "output": {"src": "hda", "id": "fa6d20d0fb68383f"}}, "stdout": "sn,mpc,gcc\n", "command_line": "ln -s \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_5.dat\" && samtools faidx `basename \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_5.dat\"` && samtools stats \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_4.dat\" --coverage 1,1000,1  --GC-depth 20000.0 --insert-size 8000    --most-inserts 0.99 --trim-quality 0 --ref-seq \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_5.dat\" > \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" && mkdir split && echo sn,mpc,gcc &&  echo \"# Summary Numbers\\n\"  > \"split/Summary numbers.tab\" && grep -q ^SN  \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" ; if [ $? = 0 ] ; then grep ^SN  \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" | cut -f 2- >> \"split/Summary numbers.tab\"  ; fi &&    echo \"# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches\" > \"split/Mismatches per cycle.tab\" && grep -q ^MPC \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" ; if [ $? = 0 ] ; then grep ^MPC \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" | cut -f 2- >> \"split/Mismatches per cycle.tab\" ; fi &&    echo \"# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)\" > \"split/ACGT content per cycle.tab\" && grep -q ^GCC \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" ; if [ $? = 0 ] ; then grep ^GCC \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" | cut -f 2- >> \"split/ACGT content per cycle.tab\" ; fi &&         true", "exit_code": 0, "state": "ok", "create_time": "2015-04-21T21:46:23.415078", "params": {"coverage_max": "\"1000\"", "gc_depth": "\"20000.0\"", "insert_size": "\"8000\"", "most_inserts": "\"0.99\"", "coverage_step": "\"1\"", "dbkey": "\"hg17\"", "coverage_min": "\"1\"", "read_length": "\"0\"", "trim_quality": "\"0\"", "filter_by_flags": "{\"filter_flags\": \"nofilter\", \"__current_case__\": 1}", "split_output": "{\"generate_tables\": [\"sn\", \"mpc\", \"gcc\"], \"split_output_selector\": \"yes\", \"__current_case__\": 1}", "use_reference": "{\"reference_source\": {\"ref_file\": 5, \"reference_source_selector\": \"history\", \"__current_case__\": 1}, \"use_ref_selector\": \"yes\", \"__current_case__\": 0}", "chromInfo": "\"/Users/marten/devel/git/galaxy/tool-data/shared/ucsc/chrom/hg17.len\"", "remove_dups": "\"False\""}, "stderr": "[fai_load] build FASTA index.\n", "job_metrics": [], "model_class": "Job", "external_id": "64605", "id": "fa6d20d0fb68383f", "user_email": "test@bx.psu.edu"}, "problem_log": "Traceback (most recent call last):\n  File \"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/case.py\", line 331, in run\n    testMethod()\n  File \"/Users/marten/devel/git/galaxy/test/functional/test_toolbox.py\", line 268, in test_tool\n    self.do_it( td )\n  File \"/Users/marten/devel/git/galaxy/test/functional/test_toolbox.py\", line 67, in do_it\n    raise e\nJobOutputsError: History item  different than expected, difference (using diff):\n( /Users/marten/devel/git/tools-devteam/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2.tab v. /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpYr1M8Csamtools_stats_out2.tab )\n--- local_file\n+++ history_data\n@@ -1,5 +1,5 @@\n-# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats\n-# The command line was:  stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /Users/anton/galaxy-git/database/files/000/dataset_9.dat /Users/anton/galaxy-git/database/files/000/dataset_10.dat\n+# This file was produced by samtools stats (1.2+htslib-1.2) and can be plotted using plot-bamstats\n+# The command line was:  stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_5.dat /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_4.dat\n # CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n CHK\t1bd20fd8\t58ad2167\t29883386\n\n-------------------- >> begin captured logging << --------------------\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/users?key=test_key HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/users/2891970512fa2d5a/api_key HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/histories HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.tools.actions.upload_common: INFO: tool upload1 created job id 4\ngalaxy.tools.execute: DEBUG: Tool [upload1] created job [4] (488.979 ms)\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (4) Working directory for job is: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/4\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.handler: DEBUG: (4) Dispatching to local runner\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (4) Persisting job destination (destination id: local:///)\ngalaxy.jobs.runners: DEBUG: Job [4] queued (3770.035 ms)\ngalaxy.jobs.handler: INFO: (4) Job dispatched\ngalaxy.jobs.runners: DEBUG: (4) command is: python /Users/marten/devel/git/galaxy/tools/data_source/upload.py /Users/marten/devel/git/galaxy /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpcOV73W /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpovV4Rg 4:/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/4/dataset_4_files:/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_4.dat; return_code=$?; python /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/4/set_metadata_pDUWU1.py /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpcOV73W /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/4/galaxy.json /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/4/metadata_in_HistoryDatasetAssociation_4_KJFVUK,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/4/metadata_kwds_HistoryDatasetAssociation_4_eC_v98,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/4/metadata_out_HistoryDatasetAssociation_4_PVfJHp,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/4/metadata_results_HistoryDatasetAssociation_4_JUuyR2,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_4.dat,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/4/metadata_override_HistoryDatasetAssociation_4_OMLQxN; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (4) executing job script: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/4/galaxy_4.sh\ngalaxy.jobs: DEBUG: (4) Persisting job destination (destination id: local:///)\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/4/galaxy_4.sh\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: job 4 ended (finish() executed in (7314.557 ms))\ngalaxy.tools.actions.upload_common: INFO: tool upload1 created job id 5\ngalaxy.tools.execute: DEBUG: Tool [upload1] created job [5] (380.201 ms)\ngalaxy.jobs: DEBUG: (5) Working directory for job is: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/5\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.handler: DEBUG: (5) Dispatching to local runner\ngalaxy.jobs: DEBUG: (5) Persisting job destination (destination id: local:///)\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.runners: DEBUG: Job [5] queued (2761.054 ms)\ngalaxy.jobs.handler: INFO: (5) Job dispatched\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.runners: DEBUG: (5) command is: python /Users/marten/devel/git/galaxy/tools/data_source/upload.py /Users/marten/devel/git/galaxy /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpcOV73W /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpx_FyDt 5:/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/5/dataset_5_files:/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_5.dat; return_code=$?; python /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/5/set_metadata_ErwZWr.py /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpcOV73W /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/5/galaxy.json /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/5/metadata_in_HistoryDatasetAssociation_5_bf6GWj,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/5/metadata_kwds_HistoryDatasetAssociation_5_qdTYxt,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/5/metadata_out_HistoryDatasetAssociation_5_nILjxU,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/5/metadata_results_HistoryDatasetAssociation_5_nF9gHk,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_5.dat,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/5/metadata_override_HistoryDatasetAssociation_5_xELsea; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (5) executing job script: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/5/galaxy_5.sh\ngalaxy.jobs: DEBUG: (5) Persisting job destination (destination id: local:///)\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/5/galaxy_5.sh\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.tools.actions: INFO: Handled output (619.072 ms)\nsqlalchemy.pool.NullPool: ERROR: Exception during reset or similar\nTraceback (most recent call last):\n  File \"build/bdist.macosx-10.6-intel/egg/sqlalchemy/pool.py\", line 567, in _finalize_fairy\n    fairy._reset(pool)\n  File \"build/bdist.macosx-10.6-intel/egg/sqlalchemy/pool.py\", line 701, in _reset\n    pool._dialect.do_rollback(self)\n  File \"build/bdist.macosx-10.6-intel/egg/sqlalchemy/engine/default.py\", line 412, in do_rollback\n    dbapi_connection.rollback()\nProgrammingError: SQLite objects created in a thread can only be used in that same thread.The object was created in thread id 4568608768 and this is thread id 4471201792\nsqlalchemy.pool.NullPool: ERROR: Exception closing connection <pysqlite2.dbapi2.Connection object at 0x111207ce0>\nTraceback (most recent call last):\n  File \"build/bdist.macosx-10.6-intel/egg/sqlalchemy/pool.py\", line 251, in _close_connection\n    self._dialect.do_close(connection)\n  File \"build/bdist.macosx-10.6-intel/egg/sqlalchemy/engine/default.py\", line 418, in do_close\n    dbapi_connection.close()\nProgrammingError: SQLite objects created in a thread can only be used in that same thread.The object was created in thread id 4568608768 and this is thread id 4471201792\ngalaxy.jobs: DEBUG: job 5 ended (finish() executed in (6572.427 ms))\ngalaxy.tools.actions: INFO: Verified access to datasets (340.159 ms)\ngalaxy.tools.execute: DEBUG: Tool [samtools_stats] created job [6] (4823.769 ms)\ngalaxy.jobs: DEBUG: (6) Working directory for job is: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/6\ngalaxy.jobs.handler: DEBUG: (6) Dispatching to local runner\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (6) Persisting job destination (destination id: local:///)\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/fa6d20d0fb68383f?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\ngalaxy.jobs.runners: DEBUG: Job [6] queued (3581.802 ms)\ngalaxy.jobs.handler: INFO: (6) Job dispatched\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/fa6d20d0fb68383f?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/fa6d20d0fb68383f?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/fa6d20d0fb68383f?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\ngalaxy.jobs.runners: DEBUG: (6) command is: samtools --version | head -n 1 | awk '{ print $2 }' > /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/GALAXY_VERSION_STRING_6 2>&1; ln -s \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_5.dat\" && samtools faidx `basename \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_5.dat\"` && samtools stats \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_4.dat\" --coverage 1,1000,1  --GC-depth 20000.0 --insert-size 8000    --most-inserts 0.99 --trim-quality 0 --ref-seq \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_5.dat\" > \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" && mkdir split && echo sn,mpc,gcc &&  echo \"# Summary Numbers\\n\"  > \"split/Summary numbers.tab\" && grep -q ^SN  \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" ; if [ $? = 0 ] ; then grep ^SN  \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" | cut -f 2- >> \"split/Summary numbers.tab\"  ; fi &&    echo \"# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches\" > \"split/Mismatches per cycle.tab\" && grep -q ^MPC \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" ; if [ $? = 0 ] ; then grep ^MPC \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" | cut -f 2- >> \"split/Mismatches per cycle.tab\" ; fi &&    echo \"# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)\" > \"split/ACGT content per cycle.tab\" && grep -q ^GCC \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" ; if [ $? = 0 ] ; then grep ^GCC \"/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat\" | cut -f 2- >> \"split/ACGT content per cycle.tab\" ; fi &&         true; return_code=$?; python /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/6/set_metadata_LSTtun.py /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpcOV73W /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/6/galaxy.json /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/6/metadata_in_HistoryDatasetAssociation_6_uh9zmy,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/6/metadata_kwds_HistoryDatasetAssociation_6_6GLt0N,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/6/metadata_out_HistoryDatasetAssociation_6_OK7DHx,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/6/metadata_results_HistoryDatasetAssociation_6_GeXlkW,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/files/000/dataset_6.dat,/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/6/metadata_override_HistoryDatasetAssociation_6_ZyuaJN; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (6) executing job script: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/6/galaxy_6.sh\ngalaxy.jobs: DEBUG: (6) Persisting job destination (destination id: local:///)\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/fa6d20d0fb68383f?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/job_working_directory/000/6/galaxy_6.sh\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/fa6d20d0fb68383f?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: job 6 ended (finish() executed in (6680.679 ms))\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/fa6d20d0fb68383f?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/fa6d20d0fb68383f?full=true&key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/fa6d20d0fb68383f?key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525/contents/fa6d20d0fb68383f/display?raw=true&key=73391df1185a0911acd55c3f7fae680e HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/jobfiles, ofn: /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/jobfiles/samtools_stats_out2.tab\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/jobfiles. saved /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/jobfiles/samtools_stats_out2.tab\nbase.twilltestcase: INFO: ## files diff on /Users/marten/devel/git/tools-devteam/tool_collections/samtools/samtools_stats/test-data/samtools_stats_out2.tab and /var/folders/2z/ntdb9g2n7tq6_bcq4dj9hj9r0000gn/T/tmp69oNhW/tmp/tmpYr1M8Csamtools_stats_out2.tab lines_diff=2, found diff = 4\n--------------------- >> end captured logging << ---------------------\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_samtools_stats.test_tool_000001", "has_data": true}], "version": "0.1", "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 2, "num_tests": 2}};
        renderTestResults(test_data);
      }
    </script>
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