Mercurial > repos > lecorguille > camera_annotate
changeset 10:01a900f2e464 draft
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
| author | lecorguille |
|---|---|
| date | Tue, 12 Apr 2016 04:11:58 -0400 |
| parents | c02d80efba80 |
| children | d33e0ed5f32a |
| files | macros.xml qsub.err qsub.out |
| diffstat | 3 files changed, 1623 insertions(+), 1 deletions(-) [+] |
line wrap: on
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--- a/macros.xml Sun Apr 10 08:14:59 2016 -0400 +++ b/macros.xml Tue Apr 12 04:11:58 2016 -0400 @@ -4,7 +4,7 @@ <requirements> <requirement type="package" version="3.1.2">R</requirement> <requirement type="package" version="0.4_1">r-snow</requirement> - <requirement type="package" version="1.44.0">bioconductor-camera</requirement> + <requirement type="package" version="1.22.0">bioconductor-camera</requirement> <requirement type="package" version="1.1_4">r-batch</requirement> <requirement type="package" version="1.3.20">graphicsmagick</requirement> </requirements>
--- /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.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qsub.out Tue Apr 12 04:11:58 2016 -0400 @@ -0,0 +1,1369 @@ +git --git-dir /home/fr2424/sib/lecorguille/.planemo/gx_repo fetch >/dev/null 2>&1 +cd /tmp/713417.1.short.q/tmp32I4oD; git clone --branch 'master' '/home/fr2424/sib/lecorguille/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS} +Initialized empty Git repository in /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/.git/ +Set COMMON_STARTUP_ARGS to --dev-wheels +Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample +Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample +Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample +Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample +Initializing lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml from user_info.xml.sample +Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample +Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample +Initializing tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample +Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample +Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample +Initializing tool-data/add_scores.loc from add_scores.loc.sample +Initializing tool-data/alignseq.loc from alignseq.loc.sample +Initializing tool-data/all_fasta.loc from all_fasta.loc.sample +Initializing tool-data/bfast_indexes.loc from bfast_indexes.loc.sample +Initializing tool-data/binned_scores.loc from binned_scores.loc.sample +Initializing tool-data/codingSnps.loc from codingSnps.loc.sample +Initializing tool-data/encode_datasets.loc from encode_datasets.loc.sample +Initializing tool-data/faseq.loc from faseq.loc.sample +Initializing tool-data/funDo.loc from funDo.loc.sample +Initializing tool-data/liftOver.loc from liftOver.loc.sample +Initializing tool-data/maf_index.loc from maf_index.loc.sample +Initializing tool-data/maf_pairwise.loc from maf_pairwise.loc.sample +Initializing tool-data/microbial_data.loc from microbial_data.loc.sample +Initializing tool-data/mosaik_index.loc from mosaik_index.loc.sample +Initializing tool-data/ngs_sim_fasta.loc from ngs_sim_fasta.loc.sample +Initializing tool-data/perm_base_index.loc from perm_base_index.loc.sample +Initializing tool-data/perm_color_index.loc from perm_color_index.loc.sample +Initializing tool-data/phastOdds.loc from phastOdds.loc.sample +Initializing tool-data/picard_index.loc from picard_index.loc.sample +Initializing tool-data/quality_scores.loc from quality_scores.loc.sample +Initializing tool-data/regions.loc from regions.loc.sample +Initializing tool-data/sequence_index_base.loc from sequence_index_base.loc.sample +Initializing tool-data/sequence_index_color.loc from sequence_index_color.loc.sample +Initializing tool-data/sift_db.loc from sift_db.loc.sample +Initializing tool-data/srma_index.loc from srma_index.loc.sample +Initializing tool-data/twobit.loc from twobit.loc.sample +Initializing static/welcome.html from welcome.html.sample +Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv +Ignoring indexes: https://pypi.python.org/simple +Requirement already up-to-date: pip==8.0.2+gx2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages +Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) +Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) +Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) +Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) +Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) +Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) +Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) +Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) +Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) +Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) +Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) +Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) +Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) +Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) +Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) +Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) +Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) +Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) +Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) +Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) +Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) +Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) +Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) +Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) +Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) +Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) +Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) +Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) +Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) +Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) +Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) +Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) +Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) +Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) +Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) +Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) +Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) +Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) +Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) +Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) +Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) +Requirement already satisfied (use --upgrade to upgrade): nose in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1)) +Requirement already satisfied (use --upgrade to upgrade): NoseHTML in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2)) +Requirement already satisfied (use --upgrade to upgrade): twill==0.9.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) +Requirement already satisfied (use --upgrade to upgrade): mock in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): funcsigs>=1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): six>=1.9 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): pbr>=0.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): ordereddict in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from funcsigs>=1->mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Starting galaxy with command [cd /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/run.sh $COMMON_STARTUP_ARGS --daemon --wait] +Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv +Ignoring indexes: https://pypi.python.org/simple +Requirement already up-to-date: pip==8.0.2+gx2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages +Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) +Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) +Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) +Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) +Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) +Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) +Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) +Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) +Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) +Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) +Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) +Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) +Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) +Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) +Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) +Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) +Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) +Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) +Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) +Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) +Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) +Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) +Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) +Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) +Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) +Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) +Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) +Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) +Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) +Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) +Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) +Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) +Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) +Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) +Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) +Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) +Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) +Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) +Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) +Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) +Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) +Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv +.......... +Installing repositories - this may take some time... +Testing using galaxy_root /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev +Testing tools with command [cd /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.html --xunit_report_file /tmp/713417.1.short.q/tmp32I4oD/xunit.xml --structured_data_report_file /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.json -installed] +Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv +Ignoring indexes: https://pypi.python.org/simple +Requirement already up-to-date: pip==8.0.2+gx2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages +Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) +Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) +Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) +Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) +Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) +Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) +Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) +Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) +Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) +Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) +Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) +Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) +Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) +Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) +Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) +Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) +Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) +Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) +Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) +Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) +Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) +Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) +Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) +Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) +Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) +Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) +Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) +Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) +Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) +Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) +Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) +Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) +Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) +Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) +Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) +Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) +Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) +Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) +Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) +Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) +Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) +Requirement already satisfied (use --upgrade to upgrade): nose in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1)) +Requirement already satisfied (use --upgrade to upgrade): NoseHTML in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2)) +Requirement already satisfied (use --upgrade to upgrade): twill==0.9.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) +Requirement already satisfied (use --upgrade to upgrade): mock in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): funcsigs>=1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): six>=1.9 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): pbr>=0.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Requirement already satisfied (use --upgrade to upgrade): ordereddict in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from funcsigs>=1->mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) +Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv +[('app:main', 'new_file_path', '/tmp/713417.1.short.q/tmpqY2f0s/tmpcxO90Y/new_files_path_HU_Ghg'), ('app:main', 'database_connection', 'sqlite:////tmp/713417.1.short.q/tmpqY2f0s/tmpcxO90Y/database/universe.sqlite'), ('app:main', 'data_manager_config_file', 'config/data_manager_conf.xml.sample,test/functional/tools/sample_data_manager_conf.xml'), ('app:main', 'job_queue_workers', 5), ('app:main', 'log_destination', 'stdout'), ('app:main', 'allow_user_deletion', True), ('app:main', 'master_api_key', 'test_key'), ('app:main', 'tool_config_file', '/tmp/713417.1.short.q/tmpxaLrzG'), ('app:main', 'template_cache_path', '/tmp/713417.1.short.q/tmpqY2f0s/tmpcxO90Y/database/compiled_templates'), ('app:main', 'job_working_directory', '/tmp/713417.1.short.q/tmpqY2f0s/tmpcxO90Y/job_working_directory_57dU3e'), ('app:main', 'tool_dependency_dir', '/tmp/713417.1.short.q/tmp32I4oD/deps'), ('app:main', 'check_migrate_tools', False), ('app:main', 'tool_path', 'tools'), ('app:main', 'enable_beta_tool_formats', True), ('app:main', 'user_library_import_dir', None), ('app:main', 'galaxy_data_manager_data_path', '/tmp/713417.1.short.q/tmpqY2f0s/data_manager_test_tmpyMBM1q/data_manager_tool-dataLuK1sc'), ('app:main', 'tool_data_table_config_path', 'config/tool_data_table_conf.xml.sample,test/functional/tool-data/sample_tool_data_tables.xml'), ('app:main', 'file_path', '/tmp/713417.1.short.q/tmpqY2f0s/tmpcxO90Y/database/files'), ('app:main', 'datatype_converters_config_file', 'datatype_converters_conf.xml.sample'), ('app:main', 'database_auto_migrate', True), ('app:main', 'use_tasked_jobs', True), ('app:main', 'auto_configure_logging', True), ('app:main', 'tool_parse_help', False), ('app:main', 'shed_tool_data_table_config', 'config/shed_tool_data_table_conf.xml'), ('app:main', 'update_integrated_tool_panel', False), ('app:main', 'admin_users', 'test@bx.psu.edu'), ('app:main', 'template_path', 'templates'), ('app:main', 'allow_user_creation', True), ('app:main', 'use_heartbeat', False), ('app:main', 'allow_library_path_paste', True), ('app:main', 'api_allow_run_as', 'test@bx.psu.edu'), ('app:main', 'test_conf', 'test.conf'), ('app:main', 'id_secret', 'changethisinproductiontoo'), ('app:main', 'library_import_dir', None), ('app:main', 'cleanup_job', 'onsuccess'), ('app:main', 'running_functional_tests', True)] +galaxy.queue_worker INFO 2016-04-11 17:47:07,898 Initalizing main Galaxy Queue Worker on sqlalchemy+sqlite:// +tool_shed.tool_shed_registry DEBUG 2016-04-11 17:47:07,941 Loading references to tool sheds from /tmp/713417.1.short.q/tmp32I4oD/tool_sheds_conf.xml +tool_shed.tool_shed_registry DEBUG 2016-04-11 17:47:07,941 Loaded reference to tool shed: Target Shed +galaxy.app DEBUG 2016-04-11 17:47:07,942 Using "galaxy.ini" config file: /tmp/713417.1.short.q/tmpqY2f0s/functional_tests_wsgi.ini +migrate.versioning.repository DEBUG 2016-04-11 17:47:08,017 Loading repository lib/galaxy/model/migrate... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,019 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,019 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,019 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,019 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,019 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,019 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,019 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,019 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lib/galaxy/model/migrate/versions/0022_visualization_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,021 Script lib/galaxy/model/migrate/versions/0022_visualization_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,021 Loading script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,021 Script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,021 Loading script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,021 Script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,022 Loading script lib/galaxy/model/migrate/versions/0025_user_info.py... 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lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,034 Script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,034 Loading script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,034 Script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,034 Loading script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,034 Script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,034 Loading script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,034 Script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,034 Loading script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,034 Script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,034 Loading script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,034 Script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,034 Loading script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Loading script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Loading script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Loading script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Loading script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Loading script lib/galaxy/model/migrate/versions/0119_job_metrics.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Script lib/galaxy/model/migrate/versions/0119_job_metrics.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,035 Loading script lib/galaxy/model/migrate/versions/0120_dataset_collections.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Script lib/galaxy/model/migrate/versions/0120_dataset_collections.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,036 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,037 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,037 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,037 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,037 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,037 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,037 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,037 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,037 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... +migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,037 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully +migrate.versioning.repository DEBUG 2016-04-11 17:47:08,037 Repository lib/galaxy/model/migrate loaded successfully +migrate.versioning.repository DEBUG 2016-04-11 17:47:08,037 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) +galaxy.config INFO 2016-04-11 17:47:08,094 Install database targetting Galaxy's database configuration. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,134 Loading datatypes from /tmp/713417.1.short.q/tmp32I4oD/tmp/tmp-toolshed-acalpdi6aiCe +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,138 Loading datatypes from /tmp/713417.1.short.q/tmp32I4oD/tmp/tmp-toolshed-acalpdVDnexH +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,138 Exception importing proprietary code file /tmp/713417.1.short.q/tmp32I4oD/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/rdata_xcms_datatypes/bff835d58914/rdata_xcms_datatypes/binary: No module named binary +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,138 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,152 Loading datatypes from ./config/datatypes_conf.xml.sample +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,153 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,153 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,154 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,154 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,154 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,154 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,155 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,155 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,155 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,155 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,155 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,155 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,155 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,156 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,156 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,156 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,156 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,156 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,156 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,157 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,157 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,157 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,157 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,157 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,157 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,158 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,158 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,158 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,158 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,158 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,158 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,158 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,158 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,159 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,159 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,159 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,159 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,159 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,159 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,159 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,159 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,161 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,161 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,161 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,161 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,165 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,165 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,165 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,175 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,175 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,175 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,175 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,175 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,175 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,176 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,176 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,176 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,178 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,178 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,178 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,178 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,178 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,178 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,179 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,180 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,180 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,180 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,180 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,180 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,182 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,182 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,183 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,183 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,183 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,183 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,183 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,184 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,184 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,184 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,184 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,184 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,184 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,185 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,185 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,185 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,185 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,185 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,185 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,189 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,189 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,189 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,189 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,189 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,189 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,194 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,194 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,194 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,194 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,194 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,194 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,196 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,196 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,196 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,196 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,196 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,196 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,200 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,200 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Overriding conflicting datatype with extension 'rdata', using datatype from ./config/datatypes_conf.xml.sample. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,202 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,202 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,203 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,203 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,203 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,203 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,203 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,203 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Removed conflicting sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Removed conflicting sniffer for datatype 'galaxy.datatypes.images:Html' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,215 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,215 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,215 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,215 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,215 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt +galaxy.jobs WARNING 2016-04-11 17:47:08,274 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/713417.1.short.q/tmpqY2f0s/functional_tests_wsgi.ini" instead +galaxy.jobs DEBUG 2016-04-11 17:47:08,274 Loading job configuration from /tmp/713417.1.short.q/tmpqY2f0s/functional_tests_wsgi.ini +galaxy.jobs DEBUG 2016-04-11 17:47:08,274 Done loading job configuration +beaker.container DEBUG 2016-04-11 17:47:08,302 data file /tmp/713417.1.short.q/tmp32I4oD/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache +galaxy.tools.toolbox.watcher INFO 2016-04-11 17:47:08,303 Watchdog library unavailble, cannot monitor tools. +galaxy.tools.toolbox.base INFO 2016-04-11 17:47:08,303 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-11 17:47:08,314 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/config/shed_tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-11 17:47:08,352 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/empty_tool_conf.xml +galaxy.tools.toolbox.base DEBUG 2016-04-11 17:47:08,356 Loaded tool id: upload1, version: 1.1.4 into tool panel.. +galaxy.tools.toolbox.base DEBUG 2016-04-11 17:47:08,356 Loading section: Shed Installs +galaxy.tools.toolbox.base DEBUG 2016-04-11 17:47:08,541 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3, version: 2.1.3 into tool panel.... +galaxy.tools.deps DEBUG 2016-04-11 17:47:08,543 Unable to find config file './dependency_resolvers_conf.xml' +galaxy.tools.search DEBUG 2016-04-11 17:47:08,618 Starting to build toolbox index. +galaxy.tools.search DEBUG 2016-04-11 17:47:09,023 Toolbox index finished. +galaxy.tools.data_manager.manager DEBUG 2016-04-11 17:47:09,026 Loaded Data Manager: test_data_manager +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,029 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,032 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-04-11 17:47:09,034 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,034 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,035 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,035 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,036 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,038 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,039 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,042 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,042 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,048 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.display_applications.application ERROR 2016-04-11 17:47:09,051 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,051 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,051 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,058 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,067 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,068 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.display_applications.application ERROR 2016-04-11 17:47:09,071 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,071 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,073 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,076 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-04-11 17:47:09,078 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,079 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,080 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,080 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-04-11 17:47:09,083 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,083 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,083 Adding inherited display application 'ensembl_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,083 Adding inherited display application 'igv_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,084 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,084 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,084 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,084 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,084 Adding inherited display application 'ensembl_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,084 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,085 Adding inherited display application 'rviewer_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,085 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,085 Adding inherited display application 'ensembl_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,085 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,085 Adding inherited display application 'rviewer_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,085 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,086 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,086 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,086 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,086 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'ensembl_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'rviewer_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,088 Adding inherited display application 'ensembl_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,088 Adding inherited display application 'igv_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,088 Adding inherited display application 'ensembl_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,088 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,088 Adding inherited display application 'rviewer_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,088 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,090 Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,091 Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,092 Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,093 Loaded converter: CONVERTER_bed_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,094 Loaded converter: CONVERTER_bed_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,095 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,096 Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,097 Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,098 Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,099 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,101 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,102 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,103 Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,104 Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,105 Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,106 Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,107 Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,108 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,109 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,110 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,111 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,112 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,113 Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,114 Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,115 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,116 Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,117 Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,119 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,120 Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,121 Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,122 Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,123 Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,125 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,126 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,127 Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,128 Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,129 Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,130 Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,132 Loaded converter: CONVERTER_encodepeak_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,133 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,134 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,135 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,136 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,137 Loaded converter: CONVERTER_sam_to_bam +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,138 Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,139 Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,140 Loaded converter: CONVERTER_vcf_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,141 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,142 Loaded converter: CONVERTER_vcf_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,144 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,145 Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,146 Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,147 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,148 Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,149 Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,150 Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,151 Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,152 Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2016-04-11 17:47:09,154 Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2016-04-11 17:47:09,155 Loaded history export tool: __EXPORT_HISTORY__ +galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,157 VisualizationsRegistry, loaded plugin: charts +galaxy.visualization.plugins.config_parser INFO 2016-04-11 17:47:09,158 Visualizations plugin disabled: Circster. Skipping... +galaxy.visualization.plugins.config_parser INFO 2016-04-11 17:47:09,158 template syntax is deprecated: use entry_point instead +galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,159 VisualizationsRegistry, loaded plugin: csg +galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,159 VisualizationsRegistry, loaded plugin: graphview +galaxy.visualization.plugins.config_parser INFO 2016-04-11 17:47:09,160 template syntax is deprecated: use entry_point instead +galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,160 VisualizationsRegistry, loaded plugin: graphviz +galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,161 VisualizationsRegistry, loaded plugin: phyloviz +galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,162 VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.config_parser INFO 2016-04-11 17:47:09,163 Visualizations plugin disabled: Sweepster. Skipping... +galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,164 VisualizationsRegistry, loaded plugin: trackster +galaxy.tours INFO 2016-04-11 17:47:09,198 Loaded tour 'core.history' +galaxy.tours INFO 2016-04-11 17:47:09,244 Loaded tour 'core.galaxy_ui' +galaxy.jobs.manager DEBUG 2016-04-11 17:47:09,248 Starting job handler +galaxy.jobs INFO 2016-04-11 17:47:09,248 Handler 'main' will load all configured runner plugins +galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-11 17:47:09,249 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners DEBUG 2016-04-11 17:47:09,249 Starting 5 LocalRunner workers +galaxy.jobs DEBUG 2016-04-11 17:47:09,250 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' +galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-11 17:47:09,252 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners DEBUG 2016-04-11 17:47:09,252 Starting 2 TaskRunner workers +galaxy.jobs DEBUG 2016-04-11 17:47:09,253 Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks' +galaxy.jobs DEBUG 2016-04-11 17:47:09,253 Legacy destination with id 'local:///', url 'local:///' converted, got params: +galaxy.jobs.handler DEBUG 2016-04-11 17:47:09,253 Loaded job runners plugins: tasks:local +galaxy.jobs.handler INFO 2016-04-11 17:47:09,253 job handler stop queue started +galaxy.jobs.handler INFO 2016-04-11 17:47:09,272 job handler queue started +galaxy.sample_tracking.external_service_types DEBUG 2016-04-11 17:47:09,280 Loaded external_service_type: Simple unknown sequencer 1.0.0 +galaxy.sample_tracking.external_service_types DEBUG 2016-04-11 17:47:09,282 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 +galaxy.workflow.scheduling_manager DEBUG 2016-04-11 17:47:09,285 Starting workflow schedulers +functional_tests.py INFO 2016-04-11 17:47:09,287 Embedded Universe application started +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,299 Enabling 'search' controller, class: SearchController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,302 Enabling 'library_common' controller, class: LibraryCommon +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,303 Enabling 'userskeys' controller, class: User +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,305 Enabling 'request_type' controller, class: RequestType +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,306 Enabling 'tag' controller, class: TagsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,311 Enabling 'workflow' controller, class: WorkflowController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,311 Enabling 'data_manager' controller, class: DataManager +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,312 Enabling 'requests_admin' controller, class: RequestsAdmin +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,314 Enabling 'requests_common' controller, class: RequestsCommon +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,314 Enabling 'requests' controller, class: Requests +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,317 Enabling 'forms' controller, class: Forms +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,387 Enabling 'admin_toolshed' controller, class: AdminGalaxy +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,387 Enabling 'admin_toolshed' controller, class: AdminToolshed +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,388 Enabling 'root' controller, class: RootController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,389 Enabling 'admin' controller, class: AdminGalaxy +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,390 Enabling 'history' controller, class: HistoryController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,392 Enabling 'user' controller, class: User +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,392 Enabling 'library' controller, class: Library +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,393 Enabling 'biostar' controller, class: BiostarController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,393 Enabling 'external_services' controller, class: ExternalServiceController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,393 Enabling 'external_service' controller, class: ExternalService +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,395 Enabling 'visualization' controller, class: VisualizationController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,395 Enabling 'async' controller, class: ASync +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,396 Enabling 'library_admin' controller, class: LibraryAdmin +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,396 Enabling 'dataset' controller, class: DatasetInterface +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,397 Enabling 'mobile' controller, class: Mobile +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,398 Enabling 'page' controller, class: PageController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,398 Enabling 'error' controller, class: Error +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,399 Enabling 'tool_runner' controller, class: ToolRunner +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,419 Enabling 'search' API controller, class: SearchController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,420 Enabling 'libraries' API controller, class: LibrariesController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,420 Enabling 'group_roles' API controller, class: GroupRolesAPIController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,420 Enabling 'authenticate' API controller, class: AuthenticationController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,421 Enabling 'users' API controller, class: UserAPIController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,421 Enabling 'roles' API controller, class: RoleAPIController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,422 Enabling 'groups' API controller, class: GroupAPIController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,422 Enabling 'metrics' API controller, class: MetricsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,422 Enabling 'datatypes' API controller, class: DatatypesController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,423 Enabling 'history_contents' API controller, class: HistoryContentsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,423 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,424 Enabling 'tools' API controller, class: ToolsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,424 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,425 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,425 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,425 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,426 Enabling 'quotas' API controller, class: QuotaAPIController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,426 Enabling 'requests' API controller, class: RequestsAPIController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,426 Enabling 'page_revisions' API controller, class: PageRevisionsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,427 Enabling 'forms' API controller, class: FormDefinitionAPIController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,427 Enabling 'samples' API controller, class: SamplesAPIController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,427 Enabling 'pages' API controller, class: PagesController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,428 Enabling 'configuration' API controller, class: ConfigurationController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,428 Enabling 'tours' API controller, class: ToursController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,428 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,428 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,429 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,429 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,429 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,429 Enabling 'tool_data' API controller, class: ToolData +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,430 Enabling 'genomes' API controller, class: GenomesController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,430 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,431 Enabling 'folders' API controller, class: FoldersController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,431 Enabling 'library_contents' API controller, class: LibraryContentsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,432 Enabling 'workflows' API controller, class: WorkflowsAPIController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,432 Enabling 'visualizations' API controller, class: VisualizationsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,433 Enabling 'datasets' API controller, class: DatasetsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,433 Enabling 'histories' API controller, class: HistoriesController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,434 Enabling 'group_users' API controller, class: GroupUsersAPIController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,434 Enabling 'jobs' API controller, class: JobController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,435 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,435 Enabling 'history_tags' API controller, class: HistoryTagsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,435 Enabling 'workflow_tags' API controller, class: WorkflowTagsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,435 Enabling 'request_types' API controller, class: RequestTypeAPIController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,436 Enabling 'remote_files' API controller, class: RemoteFilesAPIController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,437 Enabling 'folder_contents' API controller, class: FolderContentsController +galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,437 Enabling 'job_files' API controller, class: JobFilesAPIController +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,915 Enabling 'httpexceptions' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,916 Enabling 'recursive' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,926 Enabling 'error' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,926 Enabling 'x-forwarded-host' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,926 Enabling 'Request ID' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,932 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,932 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,932 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,933 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,933 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static +galaxy.queue_worker INFO 2016-04-11 17:47:09,933 Binding and starting galaxy control worker for main +functional_tests.py DEBUG 2016-04-11 17:47:09,933 Attempting to serve app on randomly chosen port: 9522 +functional_tests.py INFO 2016-04-11 17:47:10,069 Embedded web server started +functional_tests.py INFO 2016-04-11 17:47:10,070 Functional tests will be run against localhost:9522 +galaxy.tools.toolbox.watcher INFO 2016-04-11 17:47:10,071 Watchdog library unavailble, cannot monitor tools. +galaxy.tools.toolbox.base INFO 2016-04-11 17:47:10,071 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-11 17:47:10,071 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/config/shed_tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-11 17:47:10,097 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/empty_tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-11 17:47:10,097 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/config/shed_tool_conf.xml +galaxy.tools.toolbox.base DEBUG 2016-04-11 17:47:10,175 Loaded tool id: upload1, version: 1.1.4 into tool panel.. +galaxy.tools.toolbox.base DEBUG 2016-04-11 17:47:10,175 Loading section: Shed Installs +galaxy.tools.toolbox.base DEBUG 2016-04-11 17:47:10,400 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3, version: 2.1.3 into tool panel.... +galaxy.tools.deps DEBUG 2016-04-11 17:47:10,401 Unable to find config file './dependency_resolvers_conf.xml' +[?1034hbase.asserts DEBUG 2016-04-11 17:47:10,504 base.asserts.text +base.asserts DEBUG 2016-04-11 17:47:10,505 base.asserts.tabular +base.asserts DEBUG 2016-04-11 17:47:10,505 base.asserts.xml +nose.plugins.manager DEBUG 2016-04-11 17:47:10,516 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:10,589 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-04-11 17:47:10,593 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:10,604 "GET /api/users?key=test_key HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:10,628 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-04-11 17:47:10,631 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:11,136 "POST /api/users HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:11,138 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-04-11 17:47:11,144 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:11,236 "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:11,238 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:11,438 "POST /api/histories HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:11,455 Starting new HTTP connection (1): localhost +galaxy.tools DEBUG 2016-04-11 17:47:11,695 Validated and populated state for tool request (18.524 ms) +galaxy.tools.actions.upload DEBUG 2016-04-11 17:47:11,739 Persisted uploads (20.819 ms) +galaxy.tools.actions.upload DEBUG 2016-04-11 17:47:12,160 Checked and cleaned uploads (421.017 ms) +galaxy.tools.actions.upload_common INFO 2016-04-11 17:47:12,256 tool upload1 created job id 1 +galaxy.tools.actions.upload DEBUG 2016-04-11 17:47:12,372 Created upload job (212.151 ms) +galaxy.tools.execute DEBUG 2016-04-11 17:47:12,373 Tool [upload1] created job [1] (654.615 ms) +galaxy.tools.execute DEBUG 2016-04-11 17:47:12,395 Executed all jobs for tool request: (699.689 ms) +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:12,462 "POST /api/tools HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:12,464 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:12,548 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:12,550 Starting new HTTP connection (1): localhost +galaxy.jobs DEBUG 2016-04-11 17:47:12,600 (1) Working directory for job is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1 +galaxy.jobs.handler DEBUG 2016-04-11 17:47:12,633 (1) Dispatching to local runner +galaxy.jobs DEBUG 2016-04-11 17:47:12,712 (1) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:12,734 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:12,736 Starting new HTTP connection (1): localhost +galaxy.jobs.runners DEBUG 2016-04-11 17:47:12,778 Job [1] queued (144.152 ms) +galaxy.jobs.handler INFO 2016-04-11 17:47:12,818 (1) Job dispatched +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:12,973 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:12,975 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:13,225 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:13,227 Starting new HTTP connection (1): localhost +galaxy.tools.deps DEBUG 2016-04-11 17:47:13,428 Building dependency shell command for dependency 'samtools' +galaxy.tools.deps DEBUG 2016-04-11 17:47:13,428 Find dependency samtools version None +galaxy.tools.deps DEBUG 2016-04-11 17:47:13,428 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:13,428 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:13,428 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:13,429 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:13,429 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-11 17:47:13,429 Failed to resolve dependency on 'samtools', ignoring +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:13,450 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:13,452 Starting new HTTP connection (1): localhost +galaxy.jobs.command_factory INFO 2016-04-11 17:47:13,520 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 2016-04-11 17:47:13,704 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:13,707 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:13,918 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:13,920 Starting new HTTP connection (1): localhost +galaxy.jobs.runners DEBUG 2016-04-11 17:47:13,959 (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 2016-04-11 17:47:13,974 (1) executing job script: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/galaxy_1.sh +galaxy.jobs DEBUG 2016-04-11 17:47:13,987 (1) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:14,106 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:17,054 Starting new HTTP connection (1): localhost +galaxy.jobs.runners.local DEBUG 2016-04-11 17:47:17,054 execution finished: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/galaxy_1.sh +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:17,291 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:17,294 Starting new HTTP connection (1): localhost +galaxy.datatypes.metadata DEBUG 2016-04-11 17:47:17,353 loading metadata from file for: HistoryDatasetAssociation 1 +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:17,477 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:17,479 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:17,677 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:17,679 Starting new HTTP connection (1): localhost +galaxy.tools DEBUG 2016-04-11 17:47:17,859 Validated and populated state for tool request (99.599 ms) +galaxy.jobs DEBUG 2016-04-11 17:47:17,919 job 1 ended (finish() executed in (864.203 ms)) +galaxy.tools.actions INFO 2016-04-11 17:47:18,029 Handled output (134.928 ms) +galaxy.tools.actions INFO 2016-04-11 17:47:18,101 Handled output (71.983 ms) +galaxy.tools.actions INFO 2016-04-11 17:47:18,192 Handled output (90.651 ms) +galaxy.tools.actions INFO 2016-04-11 17:47:18,283 Handled output (90.794 ms) +galaxy.tools.actions INFO 2016-04-11 17:47:18,383 Verified access to datasets (8.282 ms) +galaxy.tools.execute DEBUG 2016-04-11 17:47:18,487 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 2016-04-11 17:47:18,505 Executed all jobs for tool request: (646.356 ms) +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:18,635 "POST /api/tools HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:18,637 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:18,965 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +galaxy.jobs DEBUG 2016-04-11 17:47:19,038 (2) Working directory for job is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2 +galaxy.jobs.handler DEBUG 2016-04-11 17:47:19,056 (2) Dispatching to local runner +galaxy.jobs DEBUG 2016-04-11 17:47:19,105 (2) Persisting job destination (destination id: local:///) +galaxy.jobs.runners DEBUG 2016-04-11 17:47:19,162 Job [2] queued (106.028 ms) +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:19,189 Starting new HTTP connection (1): localhost +galaxy.jobs.handler INFO 2016-04-11 17:47:19,255 (2) Job dispatched +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:19,562 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,849 Building dependency shell command for dependency 'R' +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,849 Find dependency R version 3.1.2 +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,858 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2ac7e450d110> (isnull? False) +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,858 Building dependency shell command for dependency 'r-snow' +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,858 Find dependency r-snow version 0.4_1 +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,858 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-11 17:47:19,859 Failed to resolve dependency on 'r-snow', ignoring +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Building dependency shell command for dependency 'bioconductor-camera' +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Find dependency bioconductor-camera version 1.44.0 +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-11 17:47:19,860 Failed to resolve dependency on 'bioconductor-camera', ignoring +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Building dependency shell command for dependency 'r-batch' +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Find dependency r-batch version 1.1_4 +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-11 17:47:19,860 Failed to resolve dependency on 'r-batch', ignoring +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Building dependency shell command for dependency 'graphicsmagick' +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,861 Find dependency graphicsmagick version 1.3.20 +galaxy.tools.deps DEBUG 2016-04-11 17:47:19,861 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2ac83c0d9a50> (isnull? False) +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:19,965 Starting new HTTP connection (1): localhost +galaxy.jobs.command_factory INFO 2016-04-11 17:47:19,988 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 ${GALAXY_SLOTS:-1} sigma 6 perfwhm 0.6 maxcharge 3 maxiso 4 minfrac 0.5 ppm 5 mzabs 0.015 intval into max_peaks 100 quick FALSE polarity negative cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE multiplier 3 runDiffreport TRUE eicmax 200 eicwidth 200 value into sortpval FALSE h 480 w 640 mzdec 2 new_file_path /tmp/713417.1.short.q/tmp32I4oD/tmp/primary_5_] +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:20,213 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +galaxy.jobs.runners DEBUG 2016-04-11 17:47:20,976 (2) command is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/tool_script.sh; return_code=$?; 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 2016-04-11 17:47:20,990 (2) executing job script: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/galaxy_2.sh +galaxy.jobs DEBUG 2016-04-11 17:47:20,997 (2) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:21,018 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:21,415 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:23,019 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:23,187 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +galaxy.jobs.runners.local DEBUG 2016-04-11 17:47:23,589 execution finished: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/galaxy_2.sh +galaxy.jobs.output_checker INFO 2016-04-11 17:47:23,636 Job 2: Fatal error: Exit code 1 () +galaxy.jobs.output_checker DEBUG 2016-04-11 17:47:23,636 Tool exit code indicates an error, failing job. +galaxy.jobs DEBUG 2016-04-11 17:47:23,731 (2) setting dataset 2 state to ERROR +galaxy.jobs DEBUG 2016-04-11 17:47:23,773 (2) setting dataset 3 state to ERROR +galaxy.jobs DEBUG 2016-04-11 17:47:23,814 (2) setting dataset 4 state to ERROR +galaxy.jobs DEBUG 2016-04-11 17:47:23,858 (2) setting dataset 5 state to ERROR +galaxy.jobs DEBUG 2016-04-11 17:47:24,240 job 2 ended (finish() executed in (651.127 ms)) +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:26,393 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:26,590 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:26,592 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:26,649 "GET /api/histories/2891970512fa2d5a/contents?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:26,651 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:26,844 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:26,846 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:26,971 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:26,973 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:27,152 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:27,154 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:27,284 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:27,286 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:27,462 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:27,464 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:27,642 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:27,644 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:28,025 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:28,027 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:28,150 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:28,152 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:28,325 "GET /api/jobs/5729865256bc2525?full=true&key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:28,327 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:28,485 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None 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connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:29,087 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:29,089 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:29,213 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:29,215 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:29,395 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:29,397 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:29,520 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:29,522 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:29,733 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:29,735 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:29,863 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:29,865 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:30,034 "GET 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Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:31,046 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:31,050 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:31,227 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:31,230 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:31,355 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None +functional_tests.py INFO 2016-04-11 17:47:31,587 Shutting down +functional_tests.py INFO 2016-04-11 17:47:31,587 Shutting down embedded web server +functional_tests.py INFO 2016-04-11 17:47:31,591 Embedded web server stopped +functional_tests.py INFO 2016-04-11 17:47:31,591 Shutting down app +galaxy.jobs.handler INFO 2016-04-11 17:47:31,591 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-11 17:47:31,592 job handler queue stopped +galaxy.jobs.runners INFO 2016-04-11 17:47:31,592 TaskRunner: Sending stop signal to 2 worker threads +galaxy.jobs.runners INFO 2016-04-11 17:47:31,592 LocalRunner: Sending stop signal to 5 worker threads +galaxy.jobs.handler INFO 2016-04-11 17:47:31,592 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-11 17:47:31,593 job handler stop queue stopped +functional_tests.py INFO 2016-04-11 17:47:31,593 Embedded Universe application stopped +functional_tests.py INFO 2016-04-11 17:47:31,593 Cleaning up temporary files in /tmp/713417.1.short.q/tmpqY2f0s/tmpcxO90Y +galaxy.jobs.handler INFO 2016-04-11 17:47:32,232 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-11 17:47:32,232 job handler queue stopped +galaxy.jobs.runners INFO 2016-04-11 17:47:32,232 TaskRunner: Sending stop signal to 2 worker threads +galaxy.jobs.runners INFO 2016-04-11 17:47:32,232 LocalRunner: Sending stop signal to 5 worker threads +galaxy.jobs.handler INFO 2016-04-11 17:47:32,232 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-11 17:47:32,232 job handler stop queue stopped +testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3[0]: failed +testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3[0]: failed