Mercurial > repos > lecorguille > camera_annotate
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qsub.err Tue Apr 12 04:11:58 2016 -0400 @@ -0,0 +1,253 @@ +/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.