Mercurial > repos > lecorguille > camera_annotate
view qsub.err @ 10:01a900f2e464 draft
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
| author | lecorguille |
|---|---|
| date | Tue, 12 Apr 2016 04:11:58 -0400 |
| parents | |
| children | d33e0ed5f32a |
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/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. SNIMissingWarning /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning. InsecurePlatformWarning You are using pip version 8.0.2+gx2, however version 8.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. You are using pip version 8.0.2+gx2, however version 8.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. SNIMissingWarning /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning. InsecurePlatformWarning You are using pip version 8.0.2+gx2, however version 8.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. SNIMissingWarning /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning. InsecurePlatformWarning You are using pip version 8.0.2+gx2, however version 8.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. You are using pip version 8.0.2+gx2, however version 8.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. DEBUG:galaxy.app:python path is: /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/lib, /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/lib, /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/test, /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python27.zip, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/plat-linux2, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-old, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-dynload, /opt/6.x/python-2.7.2/lib/python2.7, /opt/6.x/python-2.7.2/lib/python2.7/plat-linux2, /opt/6.x/python-2.7.2/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages INFO:galaxy.config:Logging at '10' level to 'stdout' /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:565: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 'storage.' % (dialect.name, dialect.driver)) CAMERA.annotate ( testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 ) > Test-1 ... ERROR ====================================================================== ERROR: CAMERA.annotate ( testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/case.py", line 133, in run self.runTest(result) File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/case.py", line 151, in runTest test(result) File "/opt/6.x/python-2.7.2/lib/python2.7/unittest/case.py", line 391, in __call__ return self.run(*args, **kwds) File "/opt/6.x/python-2.7.2/lib/python2.7/unittest/case.py", line 331, in run result.addFailure(self, sys.exc_info()) File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/proxy.py", line 146, in addFailure plugins.addFailure(self.test, err) File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/plugins/manager.py", line 99, in __call__ return self.call(*arg, **kw) File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/plugins/manager.py", line 167, in simple result = meth(*arg, **kw) File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nosehtml/plugin.py", line 93, in addFailure self.print_test( 'failure', test, '\n'.join( traceback.format_exception( *error ) ) ) File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nosehtml/plugin.py", line 67, in print_test print >> f.file, "<div id='capture_%d' style='display: none'><pre class='capture'>%s</pre></div>" % ( f.counter, cgi.escape( test.capturedOutput ) ) UnicodeEncodeError: 'ascii' codec can't encode character u'\u2018' in position 413: ordinal not in range(128) -------------------- >> 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/2891970512fa2d5a/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 (18.524 ms) galaxy.tools.actions.upload: DEBUG: Persisted uploads (20.819 ms) galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (421.017 ms) galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1 galaxy.tools.actions.upload: DEBUG: Created upload job (212.151 ms) galaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (654.615 ms) galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (699.689 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/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d 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/713417.1.short.q/tmp32I4oD/job_working_directory/000/1 galaxy.jobs.handler: DEBUG: (1) Dispatching to local runner galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners: DEBUG: Job [1] queued (144.152 ms) galaxy.jobs.handler: INFO: (1) Job dispatched requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d 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=f72741b00e6cec9e3d02042b5508bb4d 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: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.command_factory: INFO: Built script [/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/tools/data_source/upload.py /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev /tmp/713417.1.short.q/tmp32I4oD/tmp/tmpIuu2Wr /tmp/713417.1.short.q/tmp32I4oD/tmp/tmpKio67E 1:/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/dataset_1_files:/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_1.dat] requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d 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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners: DEBUG: (1) command is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/set_metadata_aCYbsb.py" "/tmp/713417.1.short.q/tmp32I4oD/tmp/tmpIuu2Wr" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/galaxy.json" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_XozciK,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_PCVo6A,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_POL2Ze,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_3vJ9WJ,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_1.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_hQCXbL" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/713417.1.short.q/tmp32I4oD/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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/galaxy_1.sh requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 1 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d 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=f72741b00e6cec9e3d02042b5508bb4d 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 (99.599 ms) galaxy.jobs: DEBUG: job 1 ended (finish() executed in (864.203 ms)) galaxy.tools.actions: INFO: Handled output (134.928 ms) galaxy.tools.actions: INFO: Handled output (71.983 ms) galaxy.tools.actions: INFO: Handled output (90.651 ms) galaxy.tools.actions: INFO: Handled output (90.794 ms) galaxy.tools.actions: INFO: Verified access to datasets (8.282 ms) galaxy.tools.execute: DEBUG: Tool [testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] created job [2] (601.149 ms) galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (646.356 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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None galaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2 galaxy.jobs.handler: DEBUG: (2) Dispatching to local runner galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///) galaxy.jobs.runners: DEBUG: Job [2] queued (106.028 ms) requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.handler: INFO: (2) Job dispatched requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'R' galaxy.tools.deps: DEBUG: Find dependency R version 3.1.2 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2ac7e450d110> (isnull? False) galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'r-snow' galaxy.tools.deps: DEBUG: Find dependency r-snow version 0.4_1 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: WARNING: Failed to resolve dependency on 'r-snow', ignoring galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'bioconductor-camera' galaxy.tools.deps: DEBUG: Find dependency bioconductor-camera version 1.44.0 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: WARNING: Failed to resolve dependency on 'bioconductor-camera', ignoring galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'r-batch' galaxy.tools.deps: DEBUG: Find dependency r-batch version 1.1_4 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) galaxy.tools.deps: WARNING: Failed to resolve dependency on 'r-batch', ignoring galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'graphicsmagick' galaxy.tools.deps: DEBUG: Find dependency graphicsmagick version 1.3.20 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2ac83c0d9a50> (isnull? False) requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.command_factory: INFO: Built script [/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/713417.1.short.q/tmp32I4oD/deps/R/3.1.2/lecorguille/camera_annotate/c02d80efba80; export PACKAGE_BASE; . /tmp/713417.1.short.q/tmp32I4oD/deps/R/3.1.2/lecorguille/camera_annotate/c02d80efba80/env.sh; PACKAGE_BASE=/tmp/713417.1.short.q/tmp32I4oD/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/c02d80efba80; export PACKAGE_BASE; . /tmp/713417.1.short.q/tmp32I4oD/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/c02d80efba80/env.sh; LANG=C Rscript /tmp/713417.1.short.q/tmp32I4oD/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/c02d80efba80/camera_annotate/CAMERA.r xfunction annotatediff image /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_1.dat variableMetadataOutput /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_2.dat dataMatrixOutput /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_3.dat xsetRdataOutput /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_4.dat convert_param FALSE num_digits 0 nSlaves ${GALAXY_SLOTS:-1} sigma 6 perfwhm 0.6 maxcharge 3 maxiso 4 minfrac 0.5 ppm 5 mzabs 0.015 intval into max_peaks 100 quick FALSE polarity negative cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE multiplier 3 runDiffreport TRUE eicmax 200 eicwidth 200 value into sortpval FALSE h 480 w 640 mzdec 2 new_file_path /tmp/713417.1.short.q/tmp32I4oD/tmp/primary_5_] requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None galaxy.jobs.runners: DEBUG: (2) command is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/tool_script.sh; return_code=$?; python "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/set_metadata_7oSiGt.py" "/tmp/713417.1.short.q/tmp32I4oD/tmp/tmpIuu2Wr" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/galaxy.json" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_yQypOr,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_5pYigd,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_dqnE6s,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_bb9G1l,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_2.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_qGNTro" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_3_GFPZBf,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_3_dzMzqz,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_3_YTXBdt,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_3_60vr5_,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_3.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_3_CF9v7P" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_4_dtyp5t,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_4_0jY9lR,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_4_IYAPP7,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_4_g18Jla,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_4.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_4_YPXaBQ" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_5_w61b96,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_5_oh73F9,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_5_jXk9Pn,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_5_GgatPH,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_5.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_5_lY8WCQ" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/713417.1.short.q/tmp32I4oD/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=f72741b00e6cec9e3d02042b5508bb4d 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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/galaxy_2.sh galaxy.jobs.output_checker: INFO: Job 2: Fatal error: Exit code 1 () galaxy.jobs.output_checker: DEBUG: Tool exit code indicates an error, failing job. galaxy.jobs: DEBUG: (2) setting dataset 2 state to ERROR galaxy.jobs: DEBUG: (2) setting dataset 3 state to ERROR galaxy.jobs: DEBUG: (2) setting dataset 4 state to ERROR galaxy.jobs: DEBUG: (2) setting dataset 5 state to ERROR galaxy.jobs: DEBUG: job 2 ended (finish() executed in (651.127 ms)) requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d 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?key=f72741b00e6cec9e3d02042b5508bb4d 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?key=f72741b00e6cec9e3d02042b5508bb4d 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/provenance?key=f72741b00e6cec9e3d02042b5508bb4d 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/54f2a3a23292eb07?key=f72741b00e6cec9e3d02042b5508bb4d 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/54f2a3a23292eb07/provenance?key=f72741b00e6cec9e3d02042b5508bb4d 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/8155e4b4bf1581ff?key=f72741b00e6cec9e3d02042b5508bb4d 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/8155e4b4bf1581ff/provenance?key=f72741b00e6cec9e3d02042b5508bb4d 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/7b55dbb89df8f4e5?key=f72741b00e6cec9e3d02042b5508bb4d 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/7b55dbb89df8f4e5/provenance?key=f72741b00e6cec9e3d02042b5508bb4d 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=f72741b00e6cec9e3d02042b5508bb4d 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=f72741b00e6cec9e3d02042b5508bb4d 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?key=f72741b00e6cec9e3d02042b5508bb4d 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?key=f72741b00e6cec9e3d02042b5508bb4d 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/provenance?key=f72741b00e6cec9e3d02042b5508bb4d 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/54f2a3a23292eb07?key=f72741b00e6cec9e3d02042b5508bb4d 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/54f2a3a23292eb07/provenance?key=f72741b00e6cec9e3d02042b5508bb4d 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/8155e4b4bf1581ff?key=f72741b00e6cec9e3d02042b5508bb4d 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/8155e4b4bf1581ff/provenance?key=f72741b00e6cec9e3d02042b5508bb4d 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/7b55dbb89df8f4e5?key=f72741b00e6cec9e3d02042b5508bb4d 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/7b55dbb89df8f4e5/provenance?key=f72741b00e6cec9e3d02042b5508bb4d 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=f72741b00e6cec9e3d02042b5508bb4d 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?key=f72741b00e6cec9e3d02042b5508bb4d 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?key=f72741b00e6cec9e3d02042b5508bb4d 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/provenance?key=f72741b00e6cec9e3d02042b5508bb4d 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/54f2a3a23292eb07?key=f72741b00e6cec9e3d02042b5508bb4d 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/54f2a3a23292eb07/provenance?key=f72741b00e6cec9e3d02042b5508bb4d 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/8155e4b4bf1581ff?key=f72741b00e6cec9e3d02042b5508bb4d 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/8155e4b4bf1581ff/provenance?key=f72741b00e6cec9e3d02042b5508bb4d 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/7b55dbb89df8f4e5?key=f72741b00e6cec9e3d02042b5508bb4d 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/7b55dbb89df8f4e5/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None --------------------- >> end captured logging << --------------------- ---------------------------------------------------------------------- XML: /tmp/713417.1.short.q/tmp32I4oD/xunit.xml ---------------------------------------------------------------------- Ran 1 test in 20.783s FAILED (errors=1) cp: cannot stat `/tmp/713417.1.short.q/tmp32I4oD/jobfiles/*': No such file or directory There were problems with 2 test(s) - out of 2 test(s) executed. See /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.html for detailed breakdown.