ID: functional.test_toolbox.TestForTool_cat.test_tool_000000
Description: Concatenate datasets (for test workflows) ( cat ) > Test-1
Status: failure
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/users?key=test_key HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users/5729865256bc2525/api_key HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/histories HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.tools: DEBUG: Validated and populated state for tool request (41.843 ms)
galaxy.tools.actions.upload: DEBUG: Persisted uploads (20.623 ms)
galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (448.852 ms)
galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1
galaxy.tools.actions.upload: DEBUG: Created upload job (225.630 ms)
galaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (695.995 ms)
galaxy.tools.execute: DEBUG: Executed 1 job(s) for tool upload1 request: (734.929 ms)
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.jobs: DEBUG: (1) Working directory for job is: /tmp/tmpwwBgVs/job_working_directory/000/1
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.jobs.handler: DEBUG: (1) Dispatching to local runner
galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)
galaxy.jobs.runners: DEBUG: Job [1] queued (129.914 ms)
galaxy.jobs.handler: INFO: (1) Job dispatched
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools'
galaxy.tools.deps: DEBUG: Find dependency samtools version None
galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.jobs.command_factory: INFO: Built script [/tmp/tmpwwBgVs/job_working_directory/000/1/tool_script.sh] for tool command[python /home/john/workspace/galaxy/tools/data_source/upload.py /home/john/workspace/galaxy /tmp/tmpwwBgVs/tmp/tmpeSjJLn /tmp/tmpwwBgVs/tmp/tmplvJZM6 1:/tmp/tmpwwBgVs/job_working_directory/000/1/dataset_1_files:/tmp/tmpwwBgVs/files/000/dataset_1.dat]
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools'
galaxy.tools.deps: DEBUG: Find dependency samtools version None
galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring
galaxy.jobs.runners: DEBUG: (1) command is: mkdir -p working; cd working; /tmp/tmpwwBgVs/job_working_directory/000/1/tool_script.sh; return_code=$?; cd '/tmp/tmpwwBgVs/job_working_directory/000/1'; python "/tmp/tmpwwBgVs/job_working_directory/000/1/set_metadata_2Ah3js.py" "/tmp/tmpwwBgVs/tmp/tmpeSjJLn" "/tmp/tmpwwBgVs/job_working_directory/000/1/working/galaxy.json" "/tmp/tmpwwBgVs/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_RXN9pp,/tmp/tmpwwBgVs/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_uz8gO5,/tmp/tmpwwBgVs/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_mG60zC,/tmp/tmpwwBgVs/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_6Lkep2,/tmp/tmpwwBgVs/files/000/dataset_1.dat,/tmp/tmpwwBgVs/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_RIXczB" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/tmpwwBgVs/job_working_directory/000/1/galaxy_1.sh
galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpwwBgVs/job_working_directory/000/1/galaxy_1.sh
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.model.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 1
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.tools: DEBUG: Validated and populated state for tool request (114.852 ms)
galaxy.jobs: DEBUG: job 1 ended (finish() executed in (753.726 ms))
galaxy.tools.actions: INFO: Handled output named out_file1 for tool cat (192.326 ms)
galaxy.tools.actions: INFO: Added output datasets to history (62.733 ms)
galaxy.tools.actions: INFO: Verified access to datasets for Job[unflushed,tool_id=cat] (12.053 ms)
galaxy.tools.actions: INFO: Setup for job Job[unflushed,tool_id=cat] complete, ready to flush (30.756 ms)
galaxy.tools.actions: INFO: Flushed transaction for job Job[id=2,tool_id=cat] (72.908 ms)
galaxy.tools.execute: DEBUG: Tool [cat] created job [2] (380.756 ms)
galaxy.tools.execute: DEBUG: Executed 1 job(s) for tool cat request: (440.672 ms)
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
galaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/tmpwwBgVs/job_working_directory/000/2
galaxy.jobs.handler: DEBUG: (2) Dispatching to local runner
galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.jobs.runners: DEBUG: Job [2] queued (121.122 ms)
galaxy.jobs.handler: INFO: (2) Job dispatched
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
galaxy.jobs.command_factory: INFO: Built script [/tmp/tmpwwBgVs/job_working_directory/000/2/tool_script.sh] for tool command[cat /tmp/tmpwwBgVs/files/000/dataset_1.dat > /tmp/tmpwwBgVs/files/000/dataset_2.dat]
galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools'
galaxy.tools.deps: DEBUG: Find dependency samtools version None
galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring
galaxy.jobs.runners: DEBUG: (2) command is: mkdir -p working; cd working; /tmp/tmpwwBgVs/job_working_directory/000/2/tool_script.sh; return_code=$?; cd '/tmp/tmpwwBgVs/job_working_directory/000/2'; python "/tmp/tmpwwBgVs/job_working_directory/000/2/set_metadata_gj6rLF.py" "/tmp/tmpwwBgVs/tmp/tmpeSjJLn" "/tmp/tmpwwBgVs/job_working_directory/000/2/working/galaxy.json" "/tmp/tmpwwBgVs/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_xyfvRc,/tmp/tmpwwBgVs/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_7VahWW,/tmp/tmpwwBgVs/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_SiN6cX,/tmp/tmpwwBgVs/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_Us0uvr,/tmp/tmpwwBgVs/files/000/dataset_2.dat,/tmp/tmpwwBgVs/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_mYUpFh" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/tmpwwBgVs/job_working_directory/000/2/galaxy_2.sh
galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpwwBgVs/job_working_directory/000/2/galaxy_2.sh
galaxy.model.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 2
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
galaxy.jobs: DEBUG: job 2 ended (finish() executed in (619.008 ms))
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?full=true&key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/display?raw=true&key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
Traceback (most recent call last):
File "/usr/lib/python2.7/unittest/case.py", line 331, in run
testMethod()
File "/home/john/workspace/galaxy/test/functional/test_toolbox.py", line 299, in test_tool
self.do_it( td )
File "/home/john/workspace/galaxy/test/functional/test_toolbox.py", line 75, in do_it
raise e
JobOutputsError: History item different than expected
No line of output file was 'MooCow' (output was 'chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -
chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +
chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -
chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +
chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -
chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 -
chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 +
chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 -
chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 +
chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 -
chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 +
chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 -
chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 -
chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 +
chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 -
chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 +
chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 +
chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 -
chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 +
chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 -
chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 -
chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 +
chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 -
chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 +
chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 +
chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 -
chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 +
chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 -
chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 +
chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 -
chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 +
chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 -
chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 -
chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 +
chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 -
chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 +
chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 +
chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 -
chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 +
chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 -
chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 +
chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 -
chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 +
chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 -
chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 +
chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 -
chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 +
chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 -
chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 -
chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 +
chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 -
chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 +
chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 +
chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 -
chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 +
chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 -
chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 -
chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 +
chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 -
chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 +
chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 -
chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 +
chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 -
chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 +
chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 -
')
-------------------- >> begin captured logging << --------------------
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/users?key=test_key HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users/5729865256bc2525/api_key HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/histories HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.tools: DEBUG: Validated and populated state for tool request (41.843 ms)
galaxy.tools.actions.upload: DEBUG: Persisted uploads (20.623 ms)
galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (448.852 ms)
galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1
galaxy.tools.actions.upload: DEBUG: Created upload job (225.630 ms)
galaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (695.995 ms)
galaxy.tools.execute: DEBUG: Executed 1 job(s) for tool upload1 request: (734.929 ms)
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.jobs: DEBUG: (1) Working directory for job is: /tmp/tmpwwBgVs/job_working_directory/000/1
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.jobs.handler: DEBUG: (1) Dispatching to local runner
galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)
galaxy.jobs.runners: DEBUG: Job [1] queued (129.914 ms)
galaxy.jobs.handler: INFO: (1) Job dispatched
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools'
galaxy.tools.deps: DEBUG: Find dependency samtools version None
galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.jobs.command_factory: INFO: Built script [/tmp/tmpwwBgVs/job_working_directory/000/1/tool_script.sh] for tool command[python /home/john/workspace/galaxy/tools/data_source/upload.py /home/john/workspace/galaxy /tmp/tmpwwBgVs/tmp/tmpeSjJLn /tmp/tmpwwBgVs/tmp/tmplvJZM6 1:/tmp/tmpwwBgVs/job_working_directory/000/1/dataset_1_files:/tmp/tmpwwBgVs/files/000/dataset_1.dat]
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools'
galaxy.tools.deps: DEBUG: Find dependency samtools version None
galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring
galaxy.jobs.runners: DEBUG: (1) command is: mkdir -p working; cd working; /tmp/tmpwwBgVs/job_working_directory/000/1/tool_script.sh; return_code=$?; cd '/tmp/tmpwwBgVs/job_working_directory/000/1'; python "/tmp/tmpwwBgVs/job_working_directory/000/1/set_metadata_2Ah3js.py" "/tmp/tmpwwBgVs/tmp/tmpeSjJLn" "/tmp/tmpwwBgVs/job_working_directory/000/1/working/galaxy.json" "/tmp/tmpwwBgVs/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_RXN9pp,/tmp/tmpwwBgVs/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_uz8gO5,/tmp/tmpwwBgVs/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_mG60zC,/tmp/tmpwwBgVs/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_6Lkep2,/tmp/tmpwwBgVs/files/000/dataset_1.dat,/tmp/tmpwwBgVs/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_RIXczB" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/tmpwwBgVs/job_working_directory/000/1/galaxy_1.sh
galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpwwBgVs/job_working_directory/000/1/galaxy_1.sh
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.model.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 1
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.tools: DEBUG: Validated and populated state for tool request (114.852 ms)
galaxy.jobs: DEBUG: job 1 ended (finish() executed in (753.726 ms))
galaxy.tools.actions: INFO: Handled output named out_file1 for tool cat (192.326 ms)
galaxy.tools.actions: INFO: Added output datasets to history (62.733 ms)
galaxy.tools.actions: INFO: Verified access to datasets for Job[unflushed,tool_id=cat] (12.053 ms)
galaxy.tools.actions: INFO: Setup for job Job[unflushed,tool_id=cat] complete, ready to flush (30.756 ms)
galaxy.tools.actions: INFO: Flushed transaction for job Job[id=2,tool_id=cat] (72.908 ms)
galaxy.tools.execute: DEBUG: Tool [cat] created job [2] (380.756 ms)
galaxy.tools.execute: DEBUG: Executed 1 job(s) for tool cat request: (440.672 ms)
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
galaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/tmpwwBgVs/job_working_directory/000/2
galaxy.jobs.handler: DEBUG: (2) Dispatching to local runner
galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
galaxy.jobs.runners: DEBUG: Job [2] queued (121.122 ms)
galaxy.jobs.handler: INFO: (2) Job dispatched
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
galaxy.jobs.command_factory: INFO: Built script [/tmp/tmpwwBgVs/job_working_directory/000/2/tool_script.sh] for tool command[cat /tmp/tmpwwBgVs/files/000/dataset_1.dat > /tmp/tmpwwBgVs/files/000/dataset_2.dat]
galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools'
galaxy.tools.deps: DEBUG: Find dependency samtools version None
galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring
galaxy.jobs.runners: DEBUG: (2) command is: mkdir -p working; cd working; /tmp/tmpwwBgVs/job_working_directory/000/2/tool_script.sh; return_code=$?; cd '/tmp/tmpwwBgVs/job_working_directory/000/2'; python "/tmp/tmpwwBgVs/job_working_directory/000/2/set_metadata_gj6rLF.py" "/tmp/tmpwwBgVs/tmp/tmpeSjJLn" "/tmp/tmpwwBgVs/job_working_directory/000/2/working/galaxy.json" "/tmp/tmpwwBgVs/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_xyfvRc,/tmp/tmpwwBgVs/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_7VahWW,/tmp/tmpwwBgVs/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_SiN6cX,/tmp/tmpwwBgVs/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_Us0uvr,/tmp/tmpwwBgVs/files/000/dataset_2.dat,/tmp/tmpwwBgVs/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_mYUpFh" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/tmpwwBgVs/job_working_directory/000/2/galaxy_2.sh
galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpwwBgVs/job_working_directory/000/2/galaxy_2.sh
galaxy.model.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 2
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
galaxy.jobs: DEBUG: job 2 ended (finish() executed in (619.008 ms))
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?full=true&key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/display?raw=true&key=5723299c7bc15b8cb8b00e98a08e9203 HTTP/1.1" 200 None
--------------------- >> end captured logging << ---------------------