Mercurial > repos > mmonsoor > camera_combinexsannos
changeset 3:f5372f7c831a draft
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835-dirty
| author | lecorguille |
|---|---|
| date | Tue, 12 Apr 2016 04:14:10 -0400 |
| parents | 2591056df814 |
| children | 9a1a72ee9418 |
| files | macros.xml qsub.err qsub.out |
| diffstat | 3 files changed, 3289 insertions(+), 1 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Sun Apr 10 08:14:07 2016 -0400 +++ b/macros.xml Tue Apr 12 04:14:10 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 04:14:10 2016 -0400 @@ -0,0 +1,528 @@ +/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/713105.1.short.q/tmpP_qIg6/galaxy-dev/lib, /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/lib, /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/test, /tmp/713105.1.short.q/tmpP_qIg6/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.combinexsAnnos ( testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3 ) > Test-1 ... ERROR + +====================================================================== +ERROR: CAMERA.combinexsAnnos ( testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3 ) > 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 437: 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 (18.604 ms) +galaxy.tools.actions.upload: DEBUG: Persisted uploads (20.794 ms) +galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (421.616 ms) +galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1 +galaxy.tools.actions.upload: DEBUG: Created upload job (227.243 ms) +galaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (670.247 ms) +galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (711.689 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=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 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/713105.1.short.q/tmpP_qIg6/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=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners: DEBUG: Job [1] queued (162.272 ms) +galaxy.jobs.handler: INFO: (1) Job dispatched +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 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 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.command_factory: INFO: Built script [/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/tools/data_source/upload.py /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmp07yIbk 1:/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/dataset_1_files:/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_1.dat] +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners: DEBUG: (1) command is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/set_metadata_4tX2I5.py" "/tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/galaxy.json" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_kS0IBD,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_5pLbDY,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_ZeSkpU,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_WCkLAe,/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_1.dat,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_0JObw3" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/713105.1.short.q/tmpP_qIg6/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=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/galaxy_1.sh +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs: DEBUG: job 1 ended (finish() executed in (898.090 ms)) +galaxy.tools: DEBUG: Validated and populated state for tool request (32.481 ms) +galaxy.tools.actions.upload: DEBUG: Persisted uploads (22.787 ms) +galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (434.549 ms) +galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 2 +galaxy.tools.actions.upload: DEBUG: Created upload job (217.822 ms) +galaxy.tools.execute: DEBUG: Tool [upload1] created job [2] (675.753 ms) +galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (861.378 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=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2 +galaxy.jobs.handler: DEBUG: (2) Dispatching to local runner +galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners: DEBUG: Job [2] queued (125.385 ms) +galaxy.jobs.handler: INFO: (2) Job dispatched +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 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 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.command_factory: INFO: Built script [/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/tool_script.sh] for tool command[python /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/tools/data_source/upload.py /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmp5kH8fC 2:/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/dataset_2_files:/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_2.dat] +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners: DEBUG: (2) command is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/tool_script.sh; return_code=$?; python "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/set_metadata_2M0z36.py" "/tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/galaxy.json" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_Ai0pDn,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_buBNt6,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_dXSFS6,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_z1HNLN,/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_2.dat,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_ZRIfiw" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/galaxy_2.sh +galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/galaxy_2.sh +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 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 2 +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 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 (97.725 ms) +galaxy.tools.actions: INFO: Handled output (164.454 ms) +galaxy.jobs: DEBUG: job 2 ended (finish() executed in (990.195 ms)) +galaxy.tools.actions: INFO: Verified access to datasets (15.574 ms) +galaxy.tools.execute: DEBUG: Tool [testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3] created job [3] (392.452 ms) +galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (431.967 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/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +galaxy.jobs: DEBUG: (3) Working directory for job is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3 +galaxy.jobs.handler: DEBUG: (3) Dispatching to local runner +galaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///) +galaxy.jobs.runners: DEBUG: Job [3] queued (103.168 ms) +galaxy.jobs.handler: INFO: (3) Job dispatched +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 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 0x2b13981cb5d0> (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 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (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 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (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 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (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 0x2b13503a0710> (isnull? False) +galaxy.jobs.command_factory: INFO: Built script [/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/713105.1.short.q/tmpP_qIg6/deps/R/3.1.2/mmonsoor/camera_combinexsannos/2591056df814; export PACKAGE_BASE; . /tmp/713105.1.short.q/tmpP_qIg6/deps/R/3.1.2/mmonsoor/camera_combinexsannos/2591056df814/env.sh; PACKAGE_BASE=/tmp/713105.1.short.q/tmpP_qIg6/deps/graphicsmagick/1.3.20/mmonsoor/camera_combinexsannos/2591056df814; export PACKAGE_BASE; . /tmp/713105.1.short.q/tmpP_qIg6/deps/graphicsmagick/1.3.20/mmonsoor/camera_combinexsannos/2591056df814/env.sh; LANG=C Rscript /tmp/713105.1.short.q/tmpP_qIg6/shed_tools/testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/2591056df814/camera_combinexsannos/CAMERA.r xfunction combinexsAnnos image_pos /tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_1.dat image_neg /tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_2.dat variableMetadataOutput /tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_3.dat pos TRUE tol 2 ruleset 1,1 convert_param FALSE keep_meta TRUE] +galaxy.jobs.runners: DEBUG: (3) command is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/tool_script.sh; return_code=$?; python "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/set_metadata_d9wj8r.py" "/tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/galaxy.json" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_3_LtRgbi,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_7WM6NQ,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_3_BhIIkJ,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_3_kfKhlZ,/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_3.dat,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_3_n87Fib" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local: DEBUG: (3) executing job script: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/galaxy_3.sh +galaxy.jobs: DEBUG: (3) 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/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/galaxy_3.sh +galaxy.jobs.output_checker: INFO: Job 3: Fatal error: Exit code 1 () +galaxy.jobs.output_checker: DEBUG: Tool exit code indicates an error, failing job. +galaxy.jobs: DEBUG: (3) setting dataset 3 state to ERROR +galaxy.jobs: DEBUG: job 3 ended (finish() executed in (424.557 ms)) +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?full=true&key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 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=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +--------------------- >> end captured logging << --------------------- + +---------------------------------------------------------------------- +XML: /tmp/713105.1.short.q/tmpP_qIg6/xunit.xml +---------------------------------------------------------------------- +Ran 1 test in 23.368s + +FAILED (errors=1) +cp: cannot stat `/tmp/713105.1.short.q/tmpP_qIg6/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_combinexsannos/tool_test_output.html for detailed breakdown. +/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/713334.1.short.q/tmpsEEpi3/galaxy-dev/lib, /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/lib, /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/test, /tmp/713334.1.short.q/tmpsEEpi3/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.combinexsAnnos ( testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3 ) > Test-1 ... ERROR + +====================================================================== +ERROR: CAMERA.combinexsAnnos ( testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3 ) > 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 437: 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 (19.293 ms) +galaxy.tools.actions.upload: DEBUG: Persisted uploads (21.733 ms) +galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (465.971 ms) +galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1 +galaxy.tools.actions.upload: DEBUG: Created upload job (236.755 ms) +galaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (725.060 ms) +galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (766.715 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=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1 +galaxy.jobs.handler: DEBUG: (1) Dispatching to local runner +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///) +galaxy.jobs.runners: DEBUG: Job [1] queued (189.303 ms) +galaxy.jobs.handler: INFO: (1) Job dispatched +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.command_factory: INFO: Built script [/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/tools/data_source/upload.py /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmpfJ5r0e 1:/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/dataset_1_files:/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_1.dat] +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners: DEBUG: (1) command is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/set_metadata_JxYGz5.py" "/tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/galaxy.json" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_onqmr5,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_Pjphbp,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1__nrzej,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_vGIlJV,/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_1.dat,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_aZcMtE" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/713334.1.short.q/tmpsEEpi3/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=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/galaxy_1.sh +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs: DEBUG: job 1 ended (finish() executed in (705.703 ms)) +galaxy.tools: DEBUG: Validated and populated state for tool request (23.639 ms) +galaxy.tools.actions.upload: DEBUG: Persisted uploads (22.461 ms) +galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (440.896 ms) +galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 2 +galaxy.tools.actions.upload: DEBUG: Created upload job (237.941 ms) +galaxy.tools.execute: DEBUG: Tool [upload1] created job [2] (701.946 ms) +galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (744.709 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=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2 +galaxy.jobs.handler: DEBUG: (2) Dispatching to local runner +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///) +galaxy.jobs.runners: DEBUG: Job [2] queued (295.954 ms) +galaxy.jobs.handler: INFO: (2) Job dispatched +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.command_factory: INFO: Built script [/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/tool_script.sh] for tool command[python /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/tools/data_source/upload.py /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmpbDMWgG 2:/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/dataset_2_files:/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_2.dat] +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners: DEBUG: (2) command is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/tool_script.sh; return_code=$?; python "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/set_metadata_gjY7n6.py" "/tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/galaxy.json" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_uRgY4O,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_GAZWhy,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_m7Y7NX,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_F8IJMS,/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_2.dat,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_be9LgQ" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/galaxy_2.sh +galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/galaxy_2.sh +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 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 2 +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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 (166.265 ms) +galaxy.jobs: DEBUG: job 2 ended (finish() executed in (949.551 ms)) +galaxy.tools.actions: INFO: Handled output (128.083 ms) +galaxy.tools.actions: INFO: Verified access to datasets (18.086 ms) +galaxy.tools.execute: DEBUG: Tool [testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3] created job [3] (343.920 ms) +galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (390.169 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/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +galaxy.jobs: DEBUG: (3) Working directory for job is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3 +galaxy.jobs.handler: DEBUG: (3) Dispatching to local runner +galaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///) +galaxy.jobs.runners: DEBUG: Job [3] queued (108.709 ms) +galaxy.jobs.handler: INFO: (3) Job dispatched +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 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 0x2aebec36b910> (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 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (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 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (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 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (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 0x2aebec1cd390> (isnull? False) +galaxy.jobs.command_factory: INFO: Built script [/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/713334.1.short.q/tmpsEEpi3/deps/R/3.1.2/mmonsoor/camera_combinexsannos/2591056df814; export PACKAGE_BASE; . /tmp/713334.1.short.q/tmpsEEpi3/deps/R/3.1.2/mmonsoor/camera_combinexsannos/2591056df814/env.sh; PACKAGE_BASE=/tmp/713334.1.short.q/tmpsEEpi3/deps/graphicsmagick/1.3.20/mmonsoor/camera_combinexsannos/2591056df814; export PACKAGE_BASE; . /tmp/713334.1.short.q/tmpsEEpi3/deps/graphicsmagick/1.3.20/mmonsoor/camera_combinexsannos/2591056df814/env.sh; LANG=C Rscript /tmp/713334.1.short.q/tmpsEEpi3/shed_tools/testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/2591056df814/camera_combinexsannos/CAMERA.r xfunction combinexsAnnos image_pos /tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_1.dat image_neg /tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_2.dat variableMetadataOutput /tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_3.dat pos TRUE tol 2 ruleset 1,1 convert_param FALSE keep_meta TRUE] +galaxy.jobs.runners: DEBUG: (3) command is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/tool_script.sh; return_code=$?; python "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/set_metadata_3_tNOM.py" "/tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/galaxy.json" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_3_58fsJC,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_y6cHAM,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_3_K7CNlc,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_3_EMb9Bo,/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_3.dat,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_3_fy9km1" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local: DEBUG: (3) executing job script: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/galaxy_3.sh +galaxy.jobs: DEBUG: (3) 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/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/galaxy_3.sh +galaxy.jobs.output_checker: INFO: Job 3: Fatal error: Exit code 1 () +galaxy.jobs.output_checker: DEBUG: Tool exit code indicates an error, failing job. +galaxy.jobs: DEBUG: (3) setting dataset 3 state to ERROR +galaxy.jobs: DEBUG: job 3 ended (finish() executed in (486.830 ms)) +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?full=true&key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 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=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +--------------------- >> end captured logging << --------------------- + +---------------------------------------------------------------------- +XML: /tmp/713334.1.short.q/tmpsEEpi3/xunit.xml +---------------------------------------------------------------------- +Ran 1 test in 24.127s + +FAILED (errors=1) +cp: cannot stat `/tmp/713334.1.short.q/tmpsEEpi3/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_combinexsannos/tool_test_output.html for detailed breakdown.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qsub.out Tue Apr 12 04:14:10 2016 -0400 @@ -0,0 +1,2760 @@ +git --git-dir /home/fr2424/sib/lecorguille/.planemo/gx_repo fetch >/dev/null 2>&1 +cd /tmp/713105.1.short.q/tmpP_qIg6; 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/713105.1.short.q/tmpP_qIg6/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/713105.1.short.q/tmpP_qIg6/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/713105.1.short.q/tmpP_qIg6/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/713105.1.short.q/tmpP_qIg6/galaxy-dev +Testing tools with command [cd /tmp/713105.1.short.q/tmpP_qIg6/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_combinexsannos/tool_test_output.html --xunit_report_file /tmp/713105.1.short.q/tmpP_qIg6/xunit.xml --structured_data_report_file /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_combinexsannos/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/713105.1.short.q/tmpfSGfL4/tmpPCYVSx/new_files_path_LGMvXJ'), ('app:main', 'database_connection', 'sqlite:////tmp/713105.1.short.q/tmpfSGfL4/tmpPCYVSx/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/713105.1.short.q/tmpqRgQWq'), ('app:main', 'template_cache_path', '/tmp/713105.1.short.q/tmpfSGfL4/tmpPCYVSx/database/compiled_templates'), ('app:main', 'job_working_directory', '/tmp/713105.1.short.q/tmpfSGfL4/tmpPCYVSx/job_working_directory_O4asiE'), ('app:main', 'tool_dependency_dir', '/tmp/713105.1.short.q/tmpP_qIg6/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/713105.1.short.q/tmpfSGfL4/data_manager_test_tmpV3omAY/data_manager_tool-data38f9dn'), ('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/713105.1.short.q/tmpfSGfL4/tmpPCYVSx/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 2016-04-10 16:01:48,614 Initalizing main Galaxy Queue Worker on sqlalchemy+sqlite:// +tool_shed.tool_shed_registry DEBUG 2016-04-10 16:01:48,686 Loading references to tool sheds from /tmp/713105.1.short.q/tmpP_qIg6/tool_sheds_conf.xml +tool_shed.tool_shed_registry DEBUG 2016-04-10 16:01:48,686 Loaded reference to tool shed: Target Shed +galaxy.app DEBUG 2016-04-10 16:01:48,687 Using "galaxy.ini" config file: /tmp/713105.1.short.q/tmpfSGfL4/functional_tests_wsgi.ini +migrate.versioning.repository DEBUG 2016-04-10 16:01:48,808 Loading repository lib/galaxy/model/migrate... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0014_pages.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Script lib/galaxy/model/migrate/versions/0020_library_upload_job.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Loading script lib/galaxy/model/migrate/versions/0021_user_prefs.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Script lib/galaxy/model/migrate/versions/0021_user_prefs.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Loading script lib/galaxy/model/migrate/versions/0022_visualization_tables.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Script lib/galaxy/model/migrate/versions/0022_visualization_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Loading script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Loading script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Loading script lib/galaxy/model/migrate/versions/0025_user_info.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Script lib/galaxy/model/migrate/versions/0025_user_info.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Loading script lib/galaxy/model/migrate/versions/0026_cloud_tables.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Script lib/galaxy/model/migrate/versions/0026_cloud_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Loading script lib/galaxy/model/migrate/versions/0027_request_events.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 Script lib/galaxy/model/migrate/versions/0027_request_events.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Loading script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Loading script lib/galaxy/model/migrate/versions/0029_user_actions.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Script lib/galaxy/model/migrate/versions/0029_user_actions.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Loading script lib/galaxy/model/migrate/versions/0030_history_slug_column.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Script lib/galaxy/model/migrate/versions/0030_history_slug_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Loading script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Loading script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Loading script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Loading script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,813 Script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Loading script lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Script lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Loading script lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Script lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Loading script lib/galaxy/model/migrate/versions/0037_samples_library.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Script lib/galaxy/model/migrate/versions/0037_samples_library.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Loading script lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Script lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Loading script lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Script lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Loading script lib/galaxy/model/migrate/versions/0040_page_annotations.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Script lib/galaxy/model/migrate/versions/0040_page_annotations.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Loading script lib/galaxy/model/migrate/versions/0041_workflow_invocation.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Script lib/galaxy/model/migrate/versions/0041_workflow_invocation.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,814 Loading script lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Script lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Loading script lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Script lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Loading script lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Script lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Loading script lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Script lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Loading script lib/galaxy/model/migrate/versions/0046_post_job_actions.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Script lib/galaxy/model/migrate/versions/0046_post_job_actions.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Loading script lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Script lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Loading script lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Script lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Loading script lib/galaxy/model/migrate/versions/0049_api_keys_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,815 Script lib/galaxy/model/migrate/versions/0049_api_keys_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Loading script lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Script lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Loading script lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Script lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Loading script lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Script lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Loading script lib/galaxy/model/migrate/versions/0053_item_ratings.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Script lib/galaxy/model/migrate/versions/0053_item_ratings.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Loading script lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Script lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Loading script lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Script lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Loading script lib/galaxy/model/migrate/versions/0056_workflow_outputs.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Script lib/galaxy/model/migrate/versions/0056_workflow_outputs.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,816 Loading script lib/galaxy/model/migrate/versions/0057_request_notify.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Script lib/galaxy/model/migrate/versions/0057_request_notify.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Loading script lib/galaxy/model/migrate/versions/0058_history_import_export.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Script lib/galaxy/model/migrate/versions/0058_history_import_export.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Loading script lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Script lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Loading script lib/galaxy/model/migrate/versions/0060_history_archive_import.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Script lib/galaxy/model/migrate/versions/0060_history_archive_import.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Loading script lib/galaxy/model/migrate/versions/0061_tasks.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Script lib/galaxy/model/migrate/versions/0061_tasks.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Loading script lib/galaxy/model/migrate/versions/0062_user_openid_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Script lib/galaxy/model/migrate/versions/0062_user_openid_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Loading script lib/galaxy/model/migrate/versions/0063_sequencer_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Script lib/galaxy/model/migrate/versions/0063_sequencer_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,817 Loading script lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Script lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Loading script lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Script lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Loading script lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Script lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Loading script lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Script lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Loading script lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Script lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Loading script lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Script lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Loading script lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Script lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Loading script lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,818 Script lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Loading script lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Script lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Loading script lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Script lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Loading script lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Script lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Loading script lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Script lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Loading script lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Script lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Loading script lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Script lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Loading script lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,819 Script lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Loading script lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Script lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Loading script lib/galaxy/model/migrate/versions/0080_quota_tables.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Script lib/galaxy/model/migrate/versions/0080_quota_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Loading script lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Script lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Loading script lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Script lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Loading script lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Script lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Loading script lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Script lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Loading script lib/galaxy/model/migrate/versions/0085_add_task_info.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Script lib/galaxy/model/migrate/versions/0085_add_task_info.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,820 Loading script lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Script lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Loading script lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Script lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Loading script lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Script lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Loading script lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Script lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Loading script lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Script lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Loading script lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Script lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Loading script lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Script lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Loading script lib/galaxy/model/migrate/versions/0093_add_job_params_col.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,821 Script lib/galaxy/model/migrate/versions/0093_add_job_params_col.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Loading script lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Script lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Loading script lib/galaxy/model/migrate/versions/0095_hda_subsets.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Script lib/galaxy/model/migrate/versions/0095_hda_subsets.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Loading script lib/galaxy/model/migrate/versions/0096_openid_provider.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Script lib/galaxy/model/migrate/versions/0096_openid_provider.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Loading script lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Script lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Loading script lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Script lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Loading script lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Script lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Loading script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,822 Script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Loading script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Loading script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Loading script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 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 2016-04-10 16:01:48,824 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 2016-04-10 16:01:48,824 Loading script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Loading script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Loading script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0119_job_metrics.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Script lib/galaxy/model/migrate/versions/0119_job_metrics.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0120_dataset_collections.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Script lib/galaxy/model/migrate/versions/0120_dataset_collections.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,827 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... +migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,827 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully +migrate.versioning.repository DEBUG 2016-04-10 16:01:48,827 Repository lib/galaxy/model/migrate loaded successfully +migrate.versioning.repository DEBUG 2016-04-10 16:01:48,827 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) +galaxy.config INFO 2016-04-10 16:01:48,880 Install database targetting Galaxy's database configuration. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,918 Loading datatypes from /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmp-toolshed-acalpdiNKOAF +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,922 Loading datatypes from /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmp-toolshed-acalpdIGFyy7 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,923 Exception importing proprietary code file /tmp/713105.1.short.q/tmpP_qIg6/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 2016-04-10 16:01:48,923 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,936 Loading datatypes from ./config/datatypes_conf.xml.sample +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,936 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,937 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,940 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,940 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,940 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,940 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,940 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,944 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,944 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,944 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,944 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,944 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,944 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,948 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,948 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,948 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,949 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,949 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,949 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,949 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,949 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,949 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,958 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,958 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,958 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,958 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,958 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,958 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,959 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,960 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,960 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,961 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,961 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,961 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,961 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,962 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,962 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,962 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,964 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,964 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,964 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,965 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,965 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,965 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,965 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,965 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,967 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,967 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,967 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,967 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,967 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,967 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,968 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,968 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,968 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,968 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,968 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,968 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,969 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,969 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,969 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,969 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,969 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,969 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,970 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,970 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,970 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,970 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,970 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,970 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,971 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,971 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,971 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,971 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,971 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,971 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,972 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,972 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,972 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,972 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,972 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,972 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,973 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,973 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,973 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,973 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,973 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,973 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,975 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,975 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,975 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,975 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,975 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,975 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,976 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,976 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,976 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,976 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,976 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,976 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,977 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,977 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,977 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,977 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,977 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,977 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,978 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,978 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,978 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,978 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,978 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,978 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,979 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,979 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,979 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,979 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,979 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,979 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,981 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,981 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,981 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,981 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,982 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,982 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,982 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,982 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,982 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,982 Overriding conflicting datatype with extension 'rdata', using datatype from ./config/datatypes_conf.xml.sample. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,983 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,983 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,983 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,983 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,983 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,983 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,984 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,984 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,984 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,984 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,984 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,985 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,985 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,985 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,985 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,985 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,985 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Removed conflicting sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.images:Html' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,996 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 2016-04-10 16:01:48,996 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,996 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,996 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,996 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt +galaxy.jobs WARNING 2016-04-10 16:01:49,069 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/713105.1.short.q/tmpfSGfL4/functional_tests_wsgi.ini" instead +galaxy.jobs DEBUG 2016-04-10 16:01:49,069 Loading job configuration from /tmp/713105.1.short.q/tmpfSGfL4/functional_tests_wsgi.ini +galaxy.jobs DEBUG 2016-04-10 16:01:49,069 Done loading job configuration +beaker.container DEBUG 2016-04-10 16:01:49,103 data file /tmp/713105.1.short.q/tmpP_qIg6/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache +galaxy.tools.toolbox.watcher INFO 2016-04-10 16:01:49,104 Watchdog library unavailble, cannot monitor tools. +galaxy.tools.toolbox.base INFO 2016-04-10 16:01:49,104 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-10 16:01:49,115 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/config/shed_tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-10 16:01:49,146 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/empty_tool_conf.xml +galaxy.tools.toolbox.base DEBUG 2016-04-10 16:01:49,146 Loaded tool id: upload1, version: 1.1.4 into tool panel.. +galaxy.tools.toolbox.base DEBUG 2016-04-10 16:01:49,146 Loading section: Shed Installs +galaxy.tools.toolbox.base DEBUG 2016-04-10 16:01:49,239 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tools.deps DEBUG 2016-04-10 16:01:49,241 Unable to find config file './dependency_resolvers_conf.xml' +galaxy.tools.search DEBUG 2016-04-10 16:01:49,338 Starting to build toolbox index. +galaxy.tools.search DEBUG 2016-04-10 16:01:49,730 Toolbox index finished. +galaxy.tools.data_manager.manager DEBUG 2016-04-10 16:01:49,733 Loaded Data Manager: test_data_manager +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,736 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,738 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-04-10 16:01:49,741 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,741 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,741 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,742 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,742 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,745 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,745 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,748 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,748 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,754 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.display_applications.application ERROR 2016-04-10 16:01:49,756 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,757 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,757 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,763 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,773 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,774 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.display_applications.application ERROR 2016-04-10 16:01:49,776 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,776 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,778 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,781 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-04-10 16:01:49,784 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,784 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,785 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,785 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-04-10 16:01:49,788 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,788 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,788 Adding inherited display application 'ensembl_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,788 Adding inherited display application 'igv_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'ensembl_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'rviewer_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,790 Adding inherited display application 'ensembl_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,790 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,790 Adding inherited display application 'rviewer_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,790 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,792 Adding inherited display application 'ensembl_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,792 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,792 Adding inherited display application 'rviewer_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,792 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,792 Adding inherited display application 'ensembl_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,792 Adding inherited display application 'igv_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,793 Adding inherited display application 'ensembl_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,793 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,793 Adding inherited display application 'rviewer_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,793 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,794 Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,795 Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,796 Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,797 Loaded converter: CONVERTER_bed_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,798 Loaded converter: CONVERTER_bed_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,799 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,800 Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,802 Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,802 Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,803 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,804 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,806 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,807 Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,808 Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,809 Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,810 Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,811 Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,812 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,813 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,814 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,815 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,816 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,817 Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,818 Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,819 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,820 Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,821 Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,822 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,823 Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,824 Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,825 Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,826 Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,827 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,828 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,829 Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,830 Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,831 Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,832 Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,833 Loaded converter: CONVERTER_encodepeak_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,834 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,835 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,836 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,837 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,838 Loaded converter: CONVERTER_sam_to_bam +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,839 Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,840 Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,841 Loaded converter: CONVERTER_vcf_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,842 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,843 Loaded converter: CONVERTER_vcf_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,844 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,846 Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,847 Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,848 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,848 Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,849 Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,850 Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,852 Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,854 Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2016-04-10 16:01:49,856 Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2016-04-10 16:01:49,857 Loaded history export tool: __EXPORT_HISTORY__ +galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,858 VisualizationsRegistry, loaded plugin: charts +galaxy.visualization.plugins.config_parser INFO 2016-04-10 16:01:49,859 Visualizations plugin disabled: Circster. Skipping... +galaxy.visualization.plugins.config_parser INFO 2016-04-10 16:01:49,859 template syntax is deprecated: use entry_point instead +galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,860 VisualizationsRegistry, loaded plugin: csg +galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,860 VisualizationsRegistry, loaded plugin: graphview +galaxy.visualization.plugins.config_parser INFO 2016-04-10 16:01:49,861 template syntax is deprecated: use entry_point instead +galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,861 VisualizationsRegistry, loaded plugin: graphviz +galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,862 VisualizationsRegistry, loaded plugin: phyloviz +galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,863 VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.config_parser INFO 2016-04-10 16:01:49,864 Visualizations plugin disabled: Sweepster. Skipping... +galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,864 VisualizationsRegistry, loaded plugin: trackster +galaxy.tours INFO 2016-04-10 16:01:49,898 Loaded tour 'core.history' +galaxy.tours INFO 2016-04-10 16:01:49,942 Loaded tour 'core.galaxy_ui' +galaxy.jobs.manager DEBUG 2016-04-10 16:01:49,945 Starting job handler +galaxy.jobs INFO 2016-04-10 16:01:49,945 Handler 'main' will load all configured runner plugins +galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-10 16:01:49,946 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners DEBUG 2016-04-10 16:01:49,946 Starting 5 LocalRunner workers +galaxy.jobs DEBUG 2016-04-10 16:01:49,947 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' +galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-10 16:01:49,949 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners DEBUG 2016-04-10 16:01:49,949 Starting 2 TaskRunner workers +galaxy.jobs DEBUG 2016-04-10 16:01:49,949 Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks' +galaxy.jobs DEBUG 2016-04-10 16:01:49,949 Legacy destination with id 'local:///', url 'local:///' converted, got params: +galaxy.jobs.handler DEBUG 2016-04-10 16:01:49,950 Loaded job runners plugins: tasks:local +galaxy.jobs.handler INFO 2016-04-10 16:01:49,950 job handler stop queue started +galaxy.jobs.handler INFO 2016-04-10 16:01:49,968 job handler queue started +galaxy.sample_tracking.external_service_types DEBUG 2016-04-10 16:01:49,974 Loaded external_service_type: Simple unknown sequencer 1.0.0 +galaxy.sample_tracking.external_service_types DEBUG 2016-04-10 16:01:49,976 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 +galaxy.workflow.scheduling_manager DEBUG 2016-04-10 16:01:49,980 Starting workflow schedulers +functional_tests.py INFO 2016-04-10 16:01:49,986 Embedded Universe application started +galaxy.web.framework.base DEBUG 2016-04-10 16:01:49,999 Enabling 'requests_admin' controller, class: RequestsAdmin +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,002 Enabling 'library_common' controller, class: LibraryCommon +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,002 Enabling 'error' controller, class: Error +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,002 Enabling 'async' controller, class: ASync +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,004 Enabling 'user' controller, class: User +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,004 Enabling 'request_type' controller, class: RequestType +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,005 Enabling 'tag' controller, class: TagsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,005 Enabling 'biostar' controller, class: BiostarController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,138 Enabling 'admin_toolshed' controller, class: AdminGalaxy +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,138 Enabling 'admin_toolshed' controller, class: AdminToolshed +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,139 Enabling 'data_manager' controller, class: DataManager +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,140 Enabling 'external_service' controller, class: ExternalService +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,142 Enabling 'page' controller, class: PageController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,142 Enabling 'requests_common' controller, class: RequestsCommon +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,144 Enabling 'visualization' controller, class: VisualizationController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,144 Enabling 'search' controller, class: SearchController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,145 Enabling 'dataset' controller, class: DatasetInterface +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,145 Enabling 'library' controller, class: Library +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,146 Enabling 'requests' controller, class: Requests +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,146 Enabling 'library_admin' controller, class: LibraryAdmin +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,146 Enabling 'mobile' controller, class: Mobile +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,147 Enabling 'tool_runner' controller, class: ToolRunner +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,148 Enabling 'forms' controller, class: Forms +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,148 Enabling 'admin' controller, class: AdminGalaxy +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,149 Enabling 'root' controller, class: RootController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,151 Enabling 'workflow' controller, class: WorkflowController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,151 Enabling 'external_services' controller, class: ExternalServiceController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,152 Enabling 'history' controller, class: HistoryController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,153 Enabling 'userskeys' controller, class: User +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,155 Enabling 'folders' API controller, class: FoldersController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,155 Enabling 'datatypes' API controller, class: DatatypesController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,155 Enabling 'tours' API controller, class: ToursController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,156 Enabling 'library_contents' API controller, class: LibraryContentsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,156 Enabling 'group_roles' API controller, class: GroupRolesAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,156 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,157 Enabling 'pages' API controller, class: PagesController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,157 Enabling 'folder_contents' API controller, class: FolderContentsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,157 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,158 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,158 Enabling 'history_tags' API controller, class: HistoryTagsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,158 Enabling 'workflow_tags' API controller, class: WorkflowTagsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,158 Enabling 'metrics' API controller, class: MetricsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,159 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,159 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,159 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,159 Enabling 'datasets' API controller, class: DatasetsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,160 Enabling 'histories' API controller, class: HistoriesController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,160 Enabling 'genomes' API controller, class: GenomesController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,161 Enabling 'remote_files' API controller, class: RemoteFilesAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,162 Enabling 'libraries' API controller, class: LibrariesController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,163 Enabling 'workflows' API controller, class: WorkflowsAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,163 Enabling 'groups' API controller, class: GroupAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,163 Enabling 'group_users' API controller, class: GroupUsersAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,164 Enabling 'users' API controller, class: UserAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,164 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,164 Enabling 'visualizations' API controller, class: VisualizationsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,165 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,165 Enabling 'tools' API controller, class: ToolsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,166 Enabling 'request_types' API controller, class: RequestTypeAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,185 Enabling 'search' API controller, class: SearchController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,185 Enabling 'page_revisions' API controller, class: PageRevisionsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,186 Enabling 'requests' API controller, class: RequestsAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,186 Enabling 'configuration' API controller, class: ConfigurationController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,186 Enabling 'roles' API controller, class: RoleAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,187 Enabling 'forms' API controller, class: FormDefinitionAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,187 Enabling 'tool_data' API controller, class: ToolData +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,187 Enabling 'jobs' API controller, class: JobController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,188 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,188 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,188 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,188 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,189 Enabling 'history_contents' API controller, class: HistoryContentsController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,189 Enabling 'quotas' API controller, class: QuotaAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,190 Enabling 'samples' API controller, class: SamplesAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,190 Enabling 'job_files' API controller, class: JobFilesAPIController +galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,190 Enabling 'authenticate' API controller, class: AuthenticationController +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,646 Enabling 'httpexceptions' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,647 Enabling 'recursive' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,661 Enabling 'error' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,662 Enabling 'x-forwarded-host' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,662 Enabling 'Request ID' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,669 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,670 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,670 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,670 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,670 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static +galaxy.queue_worker INFO 2016-04-10 16:01:50,671 Binding and starting galaxy control worker for main +functional_tests.py DEBUG 2016-04-10 16:01:50,680 Attempting to serve app on randomly chosen port: 8260 +functional_tests.py INFO 2016-04-10 16:01:50,810 Embedded web server started +functional_tests.py INFO 2016-04-10 16:01:50,811 Functional tests will be run against localhost:8260 +galaxy.tools.toolbox.watcher INFO 2016-04-10 16:01:50,812 Watchdog library unavailble, cannot monitor tools. +galaxy.tools.toolbox.base INFO 2016-04-10 16:01:50,812 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-10 16:01:50,812 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/config/shed_tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-10 16:01:50,838 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/empty_tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-10 16:01:50,838 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/config/shed_tool_conf.xml +galaxy.tools.toolbox.base DEBUG 2016-04-10 16:01:50,884 Loaded tool id: upload1, version: 1.1.4 into tool panel.. +galaxy.tools.toolbox.base DEBUG 2016-04-10 16:01:50,884 Loading section: Shed Installs +galaxy.tools.toolbox.base DEBUG 2016-04-10 16:01:50,971 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tools.deps DEBUG 2016-04-10 16:01:50,972 Unable to find config file './dependency_resolvers_conf.xml' +[?1034hbase.asserts DEBUG 2016-04-10 16:01:51,117 base.asserts.text +base.asserts DEBUG 2016-04-10 16:01:51,117 base.asserts.tabular +base.asserts DEBUG 2016-04-10 16:01:51,118 base.asserts.xml +nose.plugins.manager DEBUG 2016-04-10 16:01:51,134 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:51,212 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-04-10 16:01:51,216 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:51,232 "GET /api/users?key=test_key HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:51,273 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-04-10 16:01:51,277 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:51,736 "POST /api/users HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:51,737 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-04-10 16:01:51,742 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:51,808 "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:51,810 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:51,972 "POST /api/histories HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:51,993 Starting new HTTP connection (1): localhost +galaxy.tools DEBUG 2016-04-10 16:01:52,284 Validated and populated state for tool request (18.604 ms) +galaxy.tools.actions.upload DEBUG 2016-04-10 16:01:52,327 Persisted uploads (20.794 ms) +galaxy.tools.actions.upload DEBUG 2016-04-10 16:01:52,749 Checked and cleaned uploads (421.616 ms) +galaxy.tools.actions.upload_common INFO 2016-04-10 16:01:52,854 tool upload1 created job id 1 +galaxy.tools.actions.upload DEBUG 2016-04-10 16:01:52,977 Created upload job (227.243 ms) +galaxy.tools.execute DEBUG 2016-04-10 16:01:52,977 Tool [upload1] created job [1] (670.247 ms) +galaxy.tools.execute DEBUG 2016-04-10 16:01:52,996 Executed all jobs for tool request: (711.689 ms) +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:53,031 "POST /api/tools HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:53,033 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:53,118 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:53,120 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:53,212 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:53,214 Starting new HTTP connection (1): localhost +galaxy.jobs DEBUG 2016-04-10 16:01:53,274 (1) Working directory for job is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1 +galaxy.jobs.handler DEBUG 2016-04-10 16:01:53,321 (1) Dispatching to local runner +galaxy.jobs DEBUG 2016-04-10 16:01:53,425 (1) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:53,431 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:53,433 Starting new HTTP connection (1): localhost +galaxy.jobs.runners DEBUG 2016-04-10 16:01:53,483 Job [1] queued (162.272 ms) +galaxy.jobs.handler INFO 2016-04-10 16:01:53,595 (1) Job dispatched +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:53,697 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:53,699 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:53,986 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:53,988 Starting new HTTP connection (1): localhost +galaxy.tools.deps DEBUG 2016-04-10 16:01:54,120 Building dependency shell command for dependency 'samtools' +galaxy.tools.deps DEBUG 2016-04-10 16:01:54,121 Find dependency samtools version None +galaxy.tools.deps DEBUG 2016-04-10 16:01:54,121 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:01:54,121 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:01:54,121 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:01:54,123 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:01:54,124 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-10 16:01:54,124 Failed to resolve dependency on 'samtools', ignoring +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:54,145 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:54,147 Starting new HTTP connection (1): localhost +galaxy.jobs.command_factory INFO 2016-04-10 16:01:54,222 Built script [/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/tools/data_source/upload.py /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmp07yIbk 1:/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/dataset_1_files:/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_1.dat] +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:54,320 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:54,322 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:54,479 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:54,481 Starting new HTTP connection (1): localhost +galaxy.jobs.runners DEBUG 2016-04-10 16:01:54,644 (1) command is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/set_metadata_4tX2I5.py" "/tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/galaxy.json" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_kS0IBD,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_5pLbDY,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_ZeSkpU,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_WCkLAe,/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_1.dat,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_0JObw3" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local DEBUG 2016-04-10 16:01:54,658 (1) executing job script: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/galaxy_1.sh +galaxy.jobs DEBUG 2016-04-10 16:01:54,667 (1) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:54,692 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:57,700 Starting new HTTP connection (1): localhost +galaxy.jobs.runners.local DEBUG 2016-04-10 16:01:57,701 execution finished: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/galaxy_1.sh +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:57,953 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:57,955 Starting new HTTP connection (1): localhost +galaxy.datatypes.metadata DEBUG 2016-04-10 16:01:58,024 loading metadata from file for: HistoryDatasetAssociation 1 +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:58,124 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:58,127 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:58,487 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:58,505 Starting new HTTP connection (1): localhost +galaxy.jobs DEBUG 2016-04-10 16:01:58,599 job 1 ended (finish() executed in (898.090 ms)) +galaxy.tools DEBUG 2016-04-10 16:01:58,806 Validated and populated state for tool request (32.481 ms) +galaxy.tools.actions.upload DEBUG 2016-04-10 16:01:58,997 Persisted uploads (22.787 ms) +galaxy.tools.actions.upload DEBUG 2016-04-10 16:01:59,432 Checked and cleaned uploads (434.549 ms) +galaxy.tools.actions.upload_common INFO 2016-04-10 16:01:59,536 tool upload1 created job id 2 +galaxy.tools.actions.upload DEBUG 2016-04-10 16:01:59,650 Created upload job (217.822 ms) +galaxy.tools.execute DEBUG 2016-04-10 16:01:59,650 Tool [upload1] created job [2] (675.753 ms) +galaxy.tools.execute DEBUG 2016-04-10 16:01:59,668 Executed all jobs for tool request: (861.378 ms) +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:59,700 "POST /api/tools HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:59,703 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:59,782 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:59,785 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:59,870 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:59,872 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:59,954 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:59,956 Starting new HTTP connection (1): localhost +galaxy.jobs DEBUG 2016-04-10 16:02:00,032 (2) Working directory for job is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2 +galaxy.jobs.handler DEBUG 2016-04-10 16:02:00,065 (2) Dispatching to local runner +galaxy.jobs DEBUG 2016-04-10 16:02:00,127 (2) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:00,146 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:00,148 Starting new HTTP connection (1): localhost +galaxy.jobs.runners DEBUG 2016-04-10 16:02:00,191 Job [2] queued (125.385 ms) +galaxy.jobs.handler INFO 2016-04-10 16:02:00,269 (2) Job dispatched +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:00,454 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:00,456 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:00,764 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:00,768 Starting new HTTP connection (1): localhost +galaxy.tools.deps DEBUG 2016-04-10 16:02:00,909 Building dependency shell command for dependency 'samtools' +galaxy.tools.deps DEBUG 2016-04-10 16:02:00,909 Find dependency samtools version None +galaxy.tools.deps DEBUG 2016-04-10 16:02:00,909 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:00,909 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:00,909 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:00,910 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:00,910 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-10 16:02:00,910 Failed to resolve dependency on 'samtools', ignoring +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:00,922 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:00,924 Starting new HTTP connection (1): localhost +galaxy.jobs.command_factory INFO 2016-04-10 16:02:01,000 Built script [/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/tool_script.sh] for tool command[python /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/tools/data_source/upload.py /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmp5kH8fC 2:/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/dataset_2_files:/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_2.dat] +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:01,154 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:01,157 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:01,392 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:01,395 Starting new HTTP connection (1): localhost +galaxy.jobs.runners DEBUG 2016-04-10 16:02:01,543 (2) command is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/tool_script.sh; return_code=$?; python "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/set_metadata_2M0z36.py" "/tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/galaxy.json" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_Ai0pDn,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_buBNt6,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_dXSFS6,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_z1HNLN,/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_2.dat,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_ZRIfiw" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local DEBUG 2016-04-10 16:02:01,561 (2) executing job script: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/galaxy_2.sh +galaxy.jobs DEBUG 2016-04-10 16:02:01,570 (2) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:01,606 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:04,658 Starting new HTTP connection (1): localhost +galaxy.jobs.runners.local DEBUG 2016-04-10 16:02:04,658 execution finished: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/galaxy_2.sh +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:04,986 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:04,988 Starting new HTTP connection (1): localhost +galaxy.datatypes.metadata DEBUG 2016-04-10 16:02:05,001 loading metadata from file for: HistoryDatasetAssociation 2 +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:05,181 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:05,184 Starting new HTTP connection (1): localhost +galaxy.tools DEBUG 2016-04-10 16:02:05,395 Validated and populated state for tool request (97.725 ms) +galaxy.tools.actions INFO 2016-04-10 16:02:05,615 Handled output (164.454 ms) +galaxy.jobs DEBUG 2016-04-10 16:02:05,649 job 2 ended (finish() executed in (990.195 ms)) +galaxy.tools.actions INFO 2016-04-10 16:02:05,736 Verified access to datasets (15.574 ms) +galaxy.tools.execute DEBUG 2016-04-10 16:02:05,810 Tool [testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3] created job [3] (392.452 ms) +galaxy.tools.execute DEBUG 2016-04-10 16:02:05,827 Executed all jobs for tool request: (431.967 ms) +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:05,863 "POST /api/tools HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:05,864 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:06,021 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:06,223 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:06,374 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +galaxy.jobs DEBUG 2016-04-10 16:02:06,532 (3) Working directory for job is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3 +galaxy.jobs.handler DEBUG 2016-04-10 16:02:06,547 (3) Dispatching to local runner +galaxy.jobs DEBUG 2016-04-10 16:02:06,591 (3) Persisting job destination (destination id: local:///) +galaxy.jobs.runners DEBUG 2016-04-10 16:02:06,650 Job [3] queued (103.168 ms) +galaxy.jobs.handler INFO 2016-04-10 16:02:06,688 (3) Job dispatched +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:06,805 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:07,145 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,311 Building dependency shell command for dependency 'R' +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,311 Find dependency R version 3.1.2 +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b13981cb5d0> (isnull? False) +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Building dependency shell command for dependency 'r-snow' +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Find dependency r-snow version 0.4_1 +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-10 16:02:07,321 Failed to resolve dependency on 'r-snow', ignoring +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Building dependency shell command for dependency 'bioconductor-camera' +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Find dependency bioconductor-camera version 1.44.0 +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-10 16:02:07,321 Failed to resolve dependency on 'bioconductor-camera', ignoring +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Building dependency shell command for dependency 'r-batch' +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Find dependency r-batch version 1.1_4 +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-10 16:02:07,322 Failed to resolve dependency on 'r-batch', ignoring +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Building dependency shell command for dependency 'graphicsmagick' +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Find dependency graphicsmagick version 1.3.20 +galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b13503a0710> (isnull? False) +galaxy.jobs.command_factory INFO 2016-04-10 16:02:07,397 Built script [/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/713105.1.short.q/tmpP_qIg6/deps/R/3.1.2/mmonsoor/camera_combinexsannos/2591056df814; export PACKAGE_BASE; . /tmp/713105.1.short.q/tmpP_qIg6/deps/R/3.1.2/mmonsoor/camera_combinexsannos/2591056df814/env.sh; PACKAGE_BASE=/tmp/713105.1.short.q/tmpP_qIg6/deps/graphicsmagick/1.3.20/mmonsoor/camera_combinexsannos/2591056df814; export PACKAGE_BASE; . /tmp/713105.1.short.q/tmpP_qIg6/deps/graphicsmagick/1.3.20/mmonsoor/camera_combinexsannos/2591056df814/env.sh; LANG=C Rscript /tmp/713105.1.short.q/tmpP_qIg6/shed_tools/testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/2591056df814/camera_combinexsannos/CAMERA.r xfunction combinexsAnnos image_pos /tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_1.dat image_neg /tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_2.dat variableMetadataOutput /tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_3.dat pos TRUE tol 2 ruleset 1,1 convert_param FALSE keep_meta TRUE] +galaxy.jobs.runners DEBUG 2016-04-10 16:02:07,665 (3) command is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/tool_script.sh; return_code=$?; python "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/set_metadata_d9wj8r.py" "/tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/galaxy.json" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_3_LtRgbi,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_7WM6NQ,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_3_BhIIkJ,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_3_kfKhlZ,/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_3.dat,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_3_n87Fib" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local DEBUG 2016-04-10 16:02:07,677 (3) executing job script: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/galaxy_3.sh +galaxy.jobs DEBUG 2016-04-10 16:02:07,685 (3) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:07,948 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:08,104 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:09,708 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:09,906 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +galaxy.jobs.runners.local DEBUG 2016-04-10 16:02:10,324 execution finished: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/galaxy_3.sh +galaxy.jobs.output_checker INFO 2016-04-10 16:02:10,364 Job 3: Fatal error: Exit code 1 () +galaxy.jobs.output_checker DEBUG 2016-04-10 16:02:10,365 Tool exit code indicates an error, failing job. +galaxy.jobs DEBUG 2016-04-10 16:02:10,433 (3) setting dataset 3 state to ERROR +galaxy.jobs DEBUG 2016-04-10 16:02:10,749 job 3 ended (finish() executed in (424.557 ms)) +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:13,111 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:13,271 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:13,274 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:13,331 "GET /api/histories/2891970512fa2d5a/contents?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:13,333 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:13,703 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:13,706 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:13,845 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:13,847 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:14,043 "GET /api/jobs/54f2a3a23292eb07?full=true&key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:14,045 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:14,195 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:14,196 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:14,250 "GET /api/histories/2891970512fa2d5a/contents?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:14,252 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:14,438 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:14,440 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:14,557 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None +functional_tests.py INFO 2016-04-10 16:02:14,574 Shutting down +functional_tests.py INFO 2016-04-10 16:02:14,574 Shutting down embedded web server +functional_tests.py INFO 2016-04-10 16:02:14,577 Embedded web server stopped +functional_tests.py INFO 2016-04-10 16:02:14,577 Shutting down app +galaxy.jobs.handler INFO 2016-04-10 16:02:14,577 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-10 16:02:14,577 job handler queue stopped +galaxy.jobs.runners INFO 2016-04-10 16:02:14,577 TaskRunner: Sending stop signal to 2 worker threads +galaxy.jobs.runners INFO 2016-04-10 16:02:14,577 LocalRunner: Sending stop signal to 5 worker threads +galaxy.jobs.handler INFO 2016-04-10 16:02:14,578 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-10 16:02:14,578 job handler stop queue stopped +functional_tests.py INFO 2016-04-10 16:02:14,578 Embedded Universe application stopped +functional_tests.py INFO 2016-04-10 16:02:14,579 Cleaning up temporary files in /tmp/713105.1.short.q/tmpfSGfL4/tmpPCYVSx +galaxy.jobs.handler INFO 2016-04-10 16:02:15,442 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-10 16:02:15,442 job handler queue stopped +galaxy.jobs.runners INFO 2016-04-10 16:02:15,442 TaskRunner: Sending stop signal to 2 worker threads +galaxy.jobs.runners INFO 2016-04-10 16:02:15,442 LocalRunner: Sending stop signal to 5 worker threads +galaxy.jobs.handler INFO 2016-04-10 16:02:15,442 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-10 16:02:15,442 job handler stop queue stopped +testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3[0]: failed +testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3[0]: failed +git --git-dir /home/fr2424/sib/lecorguille/.planemo/gx_repo fetch >/dev/null 2>&1 +cd /tmp/713334.1.short.q/tmpsEEpi3; 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/713334.1.short.q/tmpsEEpi3/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/713334.1.short.q/tmpsEEpi3/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/713334.1.short.q/tmpsEEpi3/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/713334.1.short.q/tmpsEEpi3/galaxy-dev +Testing tools with command [cd /tmp/713334.1.short.q/tmpsEEpi3/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_combinexsannos/tool_test_output.html --xunit_report_file /tmp/713334.1.short.q/tmpsEEpi3/xunit.xml --structured_data_report_file /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_combinexsannos/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/713334.1.short.q/tmpi0htl5/tmpWnIGuv/new_files_path_KTg1gx'), ('app:main', 'database_connection', 'sqlite:////tmp/713334.1.short.q/tmpi0htl5/tmpWnIGuv/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/713334.1.short.q/tmpPqLFGI'), ('app:main', 'template_cache_path', '/tmp/713334.1.short.q/tmpi0htl5/tmpWnIGuv/database/compiled_templates'), ('app:main', 'job_working_directory', '/tmp/713334.1.short.q/tmpi0htl5/tmpWnIGuv/job_working_directory_jsZpiI'), ('app:main', 'tool_dependency_dir', '/tmp/713334.1.short.q/tmpsEEpi3/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/713334.1.short.q/tmpi0htl5/data_manager_test_tmpW7p51M/data_manager_tool-data0kK9J0'), ('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/713334.1.short.q/tmpi0htl5/tmpWnIGuv/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 15:37:49,725 Initalizing main Galaxy Queue Worker on sqlalchemy+sqlite:// +tool_shed.tool_shed_registry DEBUG 2016-04-11 15:37:49,767 Loading references to tool sheds from /tmp/713334.1.short.q/tmpsEEpi3/tool_sheds_conf.xml +tool_shed.tool_shed_registry DEBUG 2016-04-11 15:37:49,767 Loaded reference to tool shed: Target Shed +galaxy.app DEBUG 2016-04-11 15:37:49,768 Using "galaxy.ini" config file: /tmp/713334.1.short.q/tmpi0htl5/functional_tests_wsgi.ini +migrate.versioning.repository DEBUG 2016-04-11 15:37:49,845 Loading repository lib/galaxy/model/migrate... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0014_pages.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Script lib/galaxy/model/migrate/versions/0020_library_upload_job.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script lib/galaxy/model/migrate/versions/0021_user_prefs.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Script lib/galaxy/model/migrate/versions/0021_user_prefs.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script lib/galaxy/model/migrate/versions/0022_visualization_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Script lib/galaxy/model/migrate/versions/0022_visualization_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Loading script lib/galaxy/model/migrate/versions/0025_user_info.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Script lib/galaxy/model/migrate/versions/0025_user_info.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Loading script lib/galaxy/model/migrate/versions/0026_cloud_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Script lib/galaxy/model/migrate/versions/0026_cloud_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Loading script lib/galaxy/model/migrate/versions/0027_request_events.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Script lib/galaxy/model/migrate/versions/0027_request_events.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Loading script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Loading script lib/galaxy/model/migrate/versions/0029_user_actions.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Script lib/galaxy/model/migrate/versions/0029_user_actions.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Loading script lib/galaxy/model/migrate/versions/0030_history_slug_column.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Script lib/galaxy/model/migrate/versions/0030_history_slug_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,850 Loading script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,851 Script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,851 Loading script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,851 Script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,851 Loading script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,851 Script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,851 Loading script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,851 Script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,851 Loading script lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,851 Script lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,851 Loading script lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,851 Script lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,851 Loading script lib/galaxy/model/migrate/versions/0037_samples_library.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,851 Script lib/galaxy/model/migrate/versions/0037_samples_library.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Loading script lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Script lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Loading script lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Script lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Loading script lib/galaxy/model/migrate/versions/0040_page_annotations.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Script lib/galaxy/model/migrate/versions/0040_page_annotations.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Loading script lib/galaxy/model/migrate/versions/0041_workflow_invocation.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Script lib/galaxy/model/migrate/versions/0041_workflow_invocation.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Loading script lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Script lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Loading script lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Script lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Loading script lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,852 Script lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Loading script lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Script lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Loading script lib/galaxy/model/migrate/versions/0046_post_job_actions.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Script lib/galaxy/model/migrate/versions/0046_post_job_actions.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Loading script lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Script lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Loading script lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Script lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Loading script lib/galaxy/model/migrate/versions/0049_api_keys_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Script lib/galaxy/model/migrate/versions/0049_api_keys_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Loading script lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Script lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Loading script lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,853 Script lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,854 Loading script lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,854 Script lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,854 Loading script lib/galaxy/model/migrate/versions/0053_item_ratings.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,854 Script lib/galaxy/model/migrate/versions/0053_item_ratings.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,854 Loading script lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,854 Script lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,854 Loading script lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,854 Script lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,854 Loading script lib/galaxy/model/migrate/versions/0056_workflow_outputs.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,854 Script lib/galaxy/model/migrate/versions/0056_workflow_outputs.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,854 Loading script lib/galaxy/model/migrate/versions/0057_request_notify.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,854 Script lib/galaxy/model/migrate/versions/0057_request_notify.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,854 Loading script lib/galaxy/model/migrate/versions/0058_history_import_export.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,855 Script lib/galaxy/model/migrate/versions/0058_history_import_export.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,855 Loading script lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,855 Script lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,855 Loading script lib/galaxy/model/migrate/versions/0060_history_archive_import.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,855 Script lib/galaxy/model/migrate/versions/0060_history_archive_import.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,855 Loading script lib/galaxy/model/migrate/versions/0061_tasks.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,855 Script lib/galaxy/model/migrate/versions/0061_tasks.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,855 Loading script lib/galaxy/model/migrate/versions/0062_user_openid_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,855 Script lib/galaxy/model/migrate/versions/0062_user_openid_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,855 Loading script lib/galaxy/model/migrate/versions/0063_sequencer_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,855 Script lib/galaxy/model/migrate/versions/0063_sequencer_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,855 Loading script lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,855 Script lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Loading script lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Script lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Loading script lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Script lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Loading script lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Script lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Loading script lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Script lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Loading script lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Script lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Loading script lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Script lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Loading script lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,856 Script lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,857 Loading script lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,857 Script lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,857 Loading script lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,857 Script lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,857 Loading script lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,857 Script lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,857 Loading script lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,857 Script lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,857 Loading script lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,857 Script lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,857 Loading script lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,857 Script lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,857 Loading script lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Script lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Loading script lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Script lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Loading script lib/galaxy/model/migrate/versions/0080_quota_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Script lib/galaxy/model/migrate/versions/0080_quota_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Loading script lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Script lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Loading script lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Script lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Loading script lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Script lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Loading script lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Script lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,858 Loading script lib/galaxy/model/migrate/versions/0085_add_task_info.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,859 Script lib/galaxy/model/migrate/versions/0085_add_task_info.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,859 Loading script lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,859 Script lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,859 Loading script lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,859 Script lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,859 Loading script lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,859 Script lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,859 Loading script lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,859 Script lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,859 Loading script lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,859 Script lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,859 Loading script lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,859 Script lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Loading script lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Script lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Loading script lib/galaxy/model/migrate/versions/0093_add_job_params_col.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Script lib/galaxy/model/migrate/versions/0093_add_job_params_col.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Loading script lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Script lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Loading script lib/galaxy/model/migrate/versions/0095_hda_subsets.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Script lib/galaxy/model/migrate/versions/0095_hda_subsets.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Loading script lib/galaxy/model/migrate/versions/0096_openid_provider.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Script lib/galaxy/model/migrate/versions/0096_openid_provider.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Loading script lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Script lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Loading script lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,860 Script lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Loading script lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Script lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Loading script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Loading script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Loading script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Loading script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Loading script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Loading script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Loading script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Loading script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 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 15:37:49,862 Loading script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Loading script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Loading script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Loading script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 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 15:37:49,863 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 15:37:49,863 Loading script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,863 Script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,863 Loading script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,863 Script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,863 Loading script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,863 Script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,863 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 15:37:49,863 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 15:37:49,863 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,863 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,863 Loading script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,863 Script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,863 Loading script lib/galaxy/model/migrate/versions/0119_job_metrics.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Script lib/galaxy/model/migrate/versions/0119_job_metrics.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Loading script lib/galaxy/model/migrate/versions/0120_dataset_collections.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Script lib/galaxy/model/migrate/versions/0120_dataset_collections.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... +migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully +migrate.versioning.repository DEBUG 2016-04-11 15:37:49,865 Repository lib/galaxy/model/migrate loaded successfully +migrate.versioning.repository DEBUG 2016-04-11 15:37:49,865 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) +galaxy.config INFO 2016-04-11 15:37:49,921 Install database targetting Galaxy's database configuration. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,961 Loading datatypes from /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp-toolshed-acalpduZyvbh +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,965 Loading datatypes from /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp-toolshed-acalpdFPNzfa +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,965 Exception importing proprietary code file /tmp/713334.1.short.q/tmpsEEpi3/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 15:37:49,965 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,979 Loading datatypes from ./config/datatypes_conf.xml.sample +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,980 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,980 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,981 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,981 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,981 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,983 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,983 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,983 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,983 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,983 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,983 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,984 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,984 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,984 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,984 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,984 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,988 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,988 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,988 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,988 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,988 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,991 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,992 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,992 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,993 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,993 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,993 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,993 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,993 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,997 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,997 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,997 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,997 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,997 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,997 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,003 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,003 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,003 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,003 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,003 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,005 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,005 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,005 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,006 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,006 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,006 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,007 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,007 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,007 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,009 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,009 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,009 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,009 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,010 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,010 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,010 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,012 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,012 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,012 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,012 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,012 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,012 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,013 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,013 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,013 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,013 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,013 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,014 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,014 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,014 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,014 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,014 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,014 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,015 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,015 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,015 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,015 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,015 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,015 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,016 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,016 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,016 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,016 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,016 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,016 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,017 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,017 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,017 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,017 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,017 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,017 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,018 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,018 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,018 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,018 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,018 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,019 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,019 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,019 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,019 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,019 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,019 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,020 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,020 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,020 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,020 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,020 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,020 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,021 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,021 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,021 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,021 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,021 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,021 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,022 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,022 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,022 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,022 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,022 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,022 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,023 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,023 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,023 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,023 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,023 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,023 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,024 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,024 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,024 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,024 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,024 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,028 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,028 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,028 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,028 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Overriding conflicting datatype with extension 'rdata', using datatype from ./config/datatypes_conf.xml.sample. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,030 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,030 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,030 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,031 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,031 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,031 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,031 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,031 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,031 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Removed conflicting sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.images:Html' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,042 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,042 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,042 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,042 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,042 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,042 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 15:37:50,042 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 15:37:50,043 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,043 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,043 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,043 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt +galaxy.jobs WARNING 2016-04-11 15:37:50,102 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/713334.1.short.q/tmpi0htl5/functional_tests_wsgi.ini" instead +galaxy.jobs DEBUG 2016-04-11 15:37:50,102 Loading job configuration from /tmp/713334.1.short.q/tmpi0htl5/functional_tests_wsgi.ini +galaxy.jobs DEBUG 2016-04-11 15:37:50,102 Done loading job configuration +beaker.container DEBUG 2016-04-11 15:37:50,131 data file /tmp/713334.1.short.q/tmpsEEpi3/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache +galaxy.tools.toolbox.watcher INFO 2016-04-11 15:37:50,131 Watchdog library unavailble, cannot monitor tools. +galaxy.tools.toolbox.base INFO 2016-04-11 15:37:50,131 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-11 15:37:50,142 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/config/shed_tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-11 15:37:50,173 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/empty_tool_conf.xml +galaxy.tools.toolbox.base DEBUG 2016-04-11 15:37:50,177 Loaded tool id: upload1, version: 1.1.4 into tool panel.. +galaxy.tools.toolbox.base DEBUG 2016-04-11 15:37:50,177 Loading section: Shed Installs +galaxy.tools.toolbox.base DEBUG 2016-04-11 15:37:50,271 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tools.deps DEBUG 2016-04-11 15:37:50,272 Unable to find config file './dependency_resolvers_conf.xml' +galaxy.tools.search DEBUG 2016-04-11 15:37:50,347 Starting to build toolbox index. +galaxy.tools.search DEBUG 2016-04-11 15:37:50,735 Toolbox index finished. +galaxy.tools.data_manager.manager DEBUG 2016-04-11 15:37:50,737 Loaded Data Manager: test_data_manager +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,740 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,743 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-04-11 15:37:50,745 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 15:37:50,745 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,746 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,747 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,747 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,750 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,750 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,753 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,753 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,760 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.display_applications.application ERROR 2016-04-11 15:37:50,762 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 15:37:50,762 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,763 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,769 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,780 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,781 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.display_applications.application ERROR 2016-04-11 15:37:50,783 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 15:37:50,783 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,786 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,789 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-04-11 15:37:50,791 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 15:37:50,791 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,792 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,793 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-04-11 15:37:50,795 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 15:37:50,795 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,796 Adding inherited display application 'ensembl_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,796 Adding inherited display application 'igv_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,796 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'ensembl_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'rviewer_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'ensembl_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'rviewer_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'ensembl_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'rviewer_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,800 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,800 Adding inherited display application 'ensembl_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,800 Adding inherited display application 'igv_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,800 Adding inherited display application 'ensembl_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,800 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,800 Adding inherited display application 'rviewer_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,801 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,802 Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,803 Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,804 Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,805 Loaded converter: CONVERTER_bed_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,806 Loaded converter: CONVERTER_bed_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,808 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,809 Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,810 Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,811 Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,812 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,813 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,814 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,815 Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,816 Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,817 Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,818 Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,819 Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,821 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,822 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,823 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,824 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,825 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,826 Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,827 Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,828 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,829 Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,830 Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,831 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,832 Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,833 Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,834 Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,835 Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,836 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,837 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,838 Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,839 Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,840 Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,841 Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,843 Loaded converter: CONVERTER_encodepeak_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,844 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,845 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,846 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,847 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,848 Loaded converter: CONVERTER_sam_to_bam +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,849 Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,850 Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,851 Loaded converter: CONVERTER_vcf_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,852 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,853 Loaded converter: CONVERTER_vcf_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,855 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,856 Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,857 Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,858 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,859 Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,860 Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,861 Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,863 Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,864 Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2016-04-11 15:37:50,866 Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2016-04-11 15:37:50,867 Loaded history export tool: __EXPORT_HISTORY__ +galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,869 VisualizationsRegistry, loaded plugin: charts +galaxy.visualization.plugins.config_parser INFO 2016-04-11 15:37:50,870 Visualizations plugin disabled: Circster. Skipping... +galaxy.visualization.plugins.config_parser INFO 2016-04-11 15:37:50,870 template syntax is deprecated: use entry_point instead +galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,871 VisualizationsRegistry, loaded plugin: csg +galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,871 VisualizationsRegistry, loaded plugin: graphview +galaxy.visualization.plugins.config_parser INFO 2016-04-11 15:37:50,872 template syntax is deprecated: use entry_point instead +galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,872 VisualizationsRegistry, loaded plugin: graphviz +galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,873 VisualizationsRegistry, loaded plugin: phyloviz +galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,874 VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.config_parser INFO 2016-04-11 15:37:50,875 Visualizations plugin disabled: Sweepster. Skipping... +galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,876 VisualizationsRegistry, loaded plugin: trackster +galaxy.tours INFO 2016-04-11 15:37:50,922 Loaded tour 'core.galaxy_ui' +galaxy.tours INFO 2016-04-11 15:37:50,956 Loaded tour 'core.history' +galaxy.jobs.manager DEBUG 2016-04-11 15:37:50,959 Starting job handler +galaxy.jobs INFO 2016-04-11 15:37:50,959 Handler 'main' will load all configured runner plugins +galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-11 15:37:50,960 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners DEBUG 2016-04-11 15:37:50,960 Starting 5 LocalRunner workers +galaxy.jobs DEBUG 2016-04-11 15:37:50,961 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' +galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-11 15:37:50,963 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners DEBUG 2016-04-11 15:37:50,963 Starting 2 TaskRunner workers +galaxy.jobs DEBUG 2016-04-11 15:37:50,964 Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks' +galaxy.jobs DEBUG 2016-04-11 15:37:50,964 Legacy destination with id 'local:///', url 'local:///' converted, got params: +galaxy.jobs.handler DEBUG 2016-04-11 15:37:50,964 Loaded job runners plugins: tasks:local +galaxy.jobs.handler INFO 2016-04-11 15:37:50,965 job handler stop queue started +galaxy.jobs.handler INFO 2016-04-11 15:37:50,979 job handler queue started +galaxy.sample_tracking.external_service_types DEBUG 2016-04-11 15:37:50,989 Loaded external_service_type: Simple unknown sequencer 1.0.0 +galaxy.sample_tracking.external_service_types DEBUG 2016-04-11 15:37:50,990 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 +galaxy.workflow.scheduling_manager DEBUG 2016-04-11 15:37:50,994 Starting workflow schedulers +functional_tests.py INFO 2016-04-11 15:37:51,005 Embedded Universe application started +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,015 Enabling 'search' controller, class: SearchController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,019 Enabling 'admin' controller, class: AdminGalaxy +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,021 Enabling 'requests_admin' controller, class: RequestsAdmin +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,022 Enabling 'request_type' controller, class: RequestType +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,025 Enabling 'history' controller, class: HistoryController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,026 Enabling 'tool_runner' controller, class: ToolRunner +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,029 Enabling 'library_common' controller, class: LibraryCommon +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,030 Enabling 'visualization' controller, class: VisualizationController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,031 Enabling 'page' controller, class: PageController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,032 Enabling 'library' controller, class: Library +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,032 Enabling 'requests' controller, class: Requests +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,032 Enabling 'error' controller, class: Error +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,033 Enabling 'data_manager' controller, class: DataManager +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,033 Enabling 'library_admin' controller, class: LibraryAdmin +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,034 Enabling 'root' controller, class: RootController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,034 Enabling 'userskeys' controller, class: User +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,035 Enabling 'external_service' controller, class: ExternalService +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,036 Enabling 'dataset' controller, class: DatasetInterface +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,036 Enabling 'external_services' controller, class: ExternalServiceController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,038 Enabling 'biostar' controller, class: BiostarController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,039 Enabling 'user' controller, class: User +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,039 Enabling 'mobile' controller, class: Mobile +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,039 Enabling 'tag' controller, class: TagsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,039 Enabling 'requests_common' controller, class: RequestsCommon +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,040 Enabling 'forms' controller, class: Forms +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,108 Enabling 'admin_toolshed' controller, class: AdminGalaxy +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,108 Enabling 'admin_toolshed' controller, class: AdminToolshed +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,109 Enabling 'async' controller, class: ASync +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,110 Enabling 'workflow' controller, class: WorkflowController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,131 Enabling 'search' API controller, class: SearchController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,132 Enabling 'datatypes' API controller, class: DatatypesController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,132 Enabling 'group_roles' API controller, class: GroupRolesAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,132 Enabling 'pages' API controller, class: PagesController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,133 Enabling 'group_users' API controller, class: GroupUsersAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,133 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,133 Enabling 'history_tags' API controller, class: HistoryTagsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,133 Enabling 'workflow_tags' API controller, class: WorkflowTagsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,133 Enabling 'roles' API controller, class: RoleAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,134 Enabling 'users' API controller, class: UserAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,134 Enabling 'visualizations' API controller, class: VisualizationsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,135 Enabling 'library_contents' API controller, class: LibraryContentsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,136 Enabling 'history_contents' API controller, class: HistoryContentsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,136 Enabling 'authenticate' API controller, class: AuthenticationController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,137 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,137 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,137 Enabling 'jobs' API controller, class: JobController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,138 Enabling 'datasets' API controller, class: DatasetsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,138 Enabling 'configuration' API controller, class: ConfigurationController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,139 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,139 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,139 Enabling 'page_revisions' API controller, class: PageRevisionsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,140 Enabling 'requests' API controller, class: RequestsAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,140 Enabling 'folder_contents' API controller, class: FolderContentsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,140 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,141 Enabling 'tools' API controller, class: ToolsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,141 Enabling 'request_types' API controller, class: RequestTypeAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,142 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,142 Enabling 'quotas' API controller, class: QuotaAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,143 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,143 Enabling 'tool_data' API controller, class: ToolData +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,144 Enabling 'samples' API controller, class: SamplesAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,144 Enabling 'libraries' API controller, class: LibrariesController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,145 Enabling 'folders' API controller, class: FoldersController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,145 Enabling 'job_files' API controller, class: JobFilesAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,146 Enabling 'remote_files' API controller, class: RemoteFilesAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,146 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,147 Enabling 'workflows' API controller, class: WorkflowsAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,147 Enabling 'genomes' API controller, class: GenomesController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,147 Enabling 'metrics' API controller, class: MetricsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,148 Enabling 'forms' API controller, class: FormDefinitionAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,148 Enabling 'groups' API controller, class: GroupAPIController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,148 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,149 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,149 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,149 Enabling 'tours' API controller, class: ToursController +galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,150 Enabling 'histories' API controller, class: HistoriesController +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,633 Enabling 'httpexceptions' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,635 Enabling 'recursive' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,645 Enabling 'error' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,645 Enabling 'x-forwarded-host' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,645 Enabling 'Request ID' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,651 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,651 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,652 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,652 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,652 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static +galaxy.queue_worker INFO 2016-04-11 15:37:51,652 Binding and starting galaxy control worker for main +functional_tests.py DEBUG 2016-04-11 15:37:51,659 Attempting to serve app on randomly chosen port: 9960 +functional_tests.py INFO 2016-04-11 15:37:51,830 Embedded web server started +functional_tests.py INFO 2016-04-11 15:37:51,830 Functional tests will be run against localhost:9960 +galaxy.tools.toolbox.watcher INFO 2016-04-11 15:37:51,831 Watchdog library unavailble, cannot monitor tools. +galaxy.tools.toolbox.base INFO 2016-04-11 15:37:51,832 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-11 15:37:51,832 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/config/shed_tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-11 15:37:51,856 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/empty_tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-11 15:37:51,857 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/config/shed_tool_conf.xml +galaxy.tools.toolbox.base DEBUG 2016-04-11 15:37:51,902 Loaded tool id: upload1, version: 1.1.4 into tool panel.. +galaxy.tools.toolbox.base DEBUG 2016-04-11 15:37:51,902 Loading section: Shed Installs +galaxy.tools.toolbox.base DEBUG 2016-04-11 15:37:51,987 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3, version: 2.0.3 into tool panel.... +galaxy.tools.deps DEBUG 2016-04-11 15:37:51,987 Unable to find config file './dependency_resolvers_conf.xml' +[?1034hbase.asserts DEBUG 2016-04-11 15:37:52,453 base.asserts.text +base.asserts DEBUG 2016-04-11 15:37:52,454 base.asserts.tabular +base.asserts DEBUG 2016-04-11 15:37:52,454 base.asserts.xml +nose.plugins.manager DEBUG 2016-04-11 15:37:52,463 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:52,663 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-04-11 15:37:52,667 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:52,679 "GET /api/users?key=test_key HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:52,935 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-04-11 15:37:52,943 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:53,515 "POST /api/users HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:53,516 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-04-11 15:37:53,521 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:53,590 "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:53,592 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:53,748 "POST /api/histories HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:53,769 Starting new HTTP connection (1): localhost +galaxy.tools DEBUG 2016-04-11 15:37:54,037 Validated and populated state for tool request (19.293 ms) +galaxy.tools.actions.upload DEBUG 2016-04-11 15:37:54,081 Persisted uploads (21.733 ms) +galaxy.tools.actions.upload DEBUG 2016-04-11 15:37:54,548 Checked and cleaned uploads (465.971 ms) +galaxy.tools.actions.upload_common INFO 2016-04-11 15:37:54,651 tool upload1 created job id 1 +galaxy.tools.actions.upload DEBUG 2016-04-11 15:37:54,785 Created upload job (236.755 ms) +galaxy.tools.execute DEBUG 2016-04-11 15:37:54,785 Tool [upload1] created job [1] (725.060 ms) +galaxy.tools.execute DEBUG 2016-04-11 15:37:54,804 Executed all jobs for tool request: (766.715 ms) +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:54,841 "POST /api/tools HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:54,843 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:54,922 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:54,924 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,005 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,007 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,084 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,086 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,164 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,165 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,245 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,252 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,333 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,335 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,413 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,415 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,493 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,495 Starting new HTTP connection (1): localhost +galaxy.jobs DEBUG 2016-04-11 15:37:55,571 (1) Working directory for job is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1 +galaxy.jobs.handler DEBUG 2016-04-11 15:37:55,638 (1) Dispatching to local runner +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,736 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,738 Starting new HTTP connection (1): localhost +galaxy.jobs DEBUG 2016-04-11 15:37:55,744 (1) Persisting job destination (destination id: local:///) +galaxy.jobs.runners DEBUG 2016-04-11 15:37:55,828 Job [1] queued (189.303 ms) +galaxy.jobs.handler INFO 2016-04-11 15:37:55,872 (1) Job dispatched +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,995 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:56,001 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:56,257 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:56,268 Starting new HTTP connection (1): localhost +galaxy.tools.deps DEBUG 2016-04-11 15:37:56,441 Building dependency shell command for dependency 'samtools' +galaxy.tools.deps DEBUG 2016-04-11 15:37:56,441 Find dependency samtools version None +galaxy.tools.deps DEBUG 2016-04-11 15:37:56,441 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:37:56,441 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:37:56,444 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:37:56,444 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:37:56,444 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-11 15:37:56,444 Failed to resolve dependency on 'samtools', ignoring +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:56,463 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:56,465 Starting new HTTP connection (1): localhost +galaxy.jobs.command_factory INFO 2016-04-11 15:37:56,542 Built script [/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/tools/data_source/upload.py /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmpfJ5r0e 1:/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/dataset_1_files:/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_1.dat] +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:56,647 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:56,650 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:56,866 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:56,868 Starting new HTTP connection (1): localhost +galaxy.jobs.runners DEBUG 2016-04-11 15:37:57,002 (1) command is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/set_metadata_JxYGz5.py" "/tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/galaxy.json" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_onqmr5,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_Pjphbp,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1__nrzej,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_vGIlJV,/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_1.dat,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_aZcMtE" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local DEBUG 2016-04-11 15:37:57,020 (1) executing job script: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/galaxy_1.sh +galaxy.jobs DEBUG 2016-04-11 15:37:57,029 (1) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:57,053 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:00,147 Starting new HTTP connection (1): localhost +galaxy.jobs.runners.local DEBUG 2016-04-11 15:38:00,147 execution finished: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/galaxy_1.sh +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:00,404 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:00,425 Starting new HTTP connection (1): localhost +galaxy.datatypes.metadata DEBUG 2016-04-11 15:38:00,439 loading metadata from file for: HistoryDatasetAssociation 1 +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:00,568 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:00,570 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:00,723 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:00,741 Starting new HTTP connection (1): localhost +galaxy.jobs DEBUG 2016-04-11 15:38:00,856 job 1 ended (finish() executed in (705.703 ms)) +galaxy.tools DEBUG 2016-04-11 15:38:01,067 Validated and populated state for tool request (23.639 ms) +galaxy.tools.actions.upload DEBUG 2016-04-11 15:38:01,115 Persisted uploads (22.461 ms) +galaxy.tools.actions.upload DEBUG 2016-04-11 15:38:01,556 Checked and cleaned uploads (440.896 ms) +galaxy.tools.actions.upload_common INFO 2016-04-11 15:38:01,660 tool upload1 created job id 2 +galaxy.tools.actions.upload DEBUG 2016-04-11 15:38:01,794 Created upload job (237.941 ms) +galaxy.tools.execute DEBUG 2016-04-11 15:38:01,794 Tool [upload1] created job [2] (701.946 ms) +galaxy.tools.execute DEBUG 2016-04-11 15:38:01,811 Executed all jobs for tool request: (744.709 ms) +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:01,844 "POST /api/tools HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:01,846 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:01,924 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:01,926 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:02,006 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:02,009 Starting new HTTP connection (1): localhost +galaxy.jobs DEBUG 2016-04-11 15:38:02,099 (2) Working directory for job is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2 +galaxy.jobs.handler DEBUG 2016-04-11 15:38:02,149 (2) Dispatching to local runner +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:02,167 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:02,169 Starting new HTTP connection (1): localhost +galaxy.jobs DEBUG 2016-04-11 15:38:02,368 (2) Persisting job destination (destination id: local:///) +galaxy.jobs.runners DEBUG 2016-04-11 15:38:02,445 Job [2] queued (295.954 ms) +galaxy.jobs.handler INFO 2016-04-11 15:38:02,487 (2) Job dispatched +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:02,624 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:02,626 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:02,854 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:02,856 Starting new HTTP connection (1): localhost +galaxy.tools.deps DEBUG 2016-04-11 15:38:03,096 Building dependency shell command for dependency 'samtools' +galaxy.tools.deps DEBUG 2016-04-11 15:38:03,096 Find dependency samtools version None +galaxy.tools.deps DEBUG 2016-04-11 15:38:03,096 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:03,096 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:03,096 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:03,096 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:03,097 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-11 15:38:03,097 Failed to resolve dependency on 'samtools', ignoring +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:03,103 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:03,105 Starting new HTTP connection (1): localhost +galaxy.jobs.command_factory INFO 2016-04-11 15:38:03,174 Built script [/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/tool_script.sh] for tool command[python /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/tools/data_source/upload.py /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmpbDMWgG 2:/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/dataset_2_files:/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_2.dat] +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:03,239 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:03,242 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:03,407 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:03,409 Starting new HTTP connection (1): localhost +galaxy.jobs.runners DEBUG 2016-04-11 15:38:03,609 (2) command is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/tool_script.sh; return_code=$?; python "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/set_metadata_gjY7n6.py" "/tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/galaxy.json" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_uRgY4O,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_GAZWhy,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_m7Y7NX,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_F8IJMS,/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_2.dat,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_be9LgQ" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local DEBUG 2016-04-11 15:38:03,625 (2) executing job script: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/galaxy_2.sh +galaxy.jobs DEBUG 2016-04-11 15:38:03,634 (2) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:03,652 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:06,835 Starting new HTTP connection (1): localhost +galaxy.jobs.runners.local DEBUG 2016-04-11 15:38:06,835 execution finished: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/galaxy_2.sh +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:07,054 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:07,057 Starting new HTTP connection (1): localhost +galaxy.datatypes.metadata DEBUG 2016-04-11 15:38:07,115 loading metadata from file for: HistoryDatasetAssociation 2 +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:07,219 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:07,221 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:07,491 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:07,493 Starting new HTTP connection (1): localhost +galaxy.tools DEBUG 2016-04-11 15:38:07,715 Validated and populated state for tool request (166.265 ms) +galaxy.jobs DEBUG 2016-04-11 15:38:07,785 job 2 ended (finish() executed in (949.551 ms)) +galaxy.tools.actions INFO 2016-04-11 15:38:07,880 Handled output (128.083 ms) +galaxy.tools.actions INFO 2016-04-11 15:38:07,988 Verified access to datasets (18.086 ms) +galaxy.tools.execute DEBUG 2016-04-11 15:38:08,088 Tool [testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3] created job [3] (343.920 ms) +galaxy.tools.execute DEBUG 2016-04-11 15:38:08,105 Executed all jobs for tool request: (390.169 ms) +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:08,147 "POST /api/tools HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:08,150 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:08,302 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:08,504 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:08,668 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +galaxy.jobs DEBUG 2016-04-11 15:38:08,757 (3) Working directory for job is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3 +galaxy.jobs.handler DEBUG 2016-04-11 15:38:08,771 (3) Dispatching to local runner +galaxy.jobs DEBUG 2016-04-11 15:38:08,815 (3) Persisting job destination (destination id: local:///) +galaxy.jobs.runners DEBUG 2016-04-11 15:38:08,880 Job [3] queued (108.709 ms) +galaxy.jobs.handler INFO 2016-04-11 15:38:08,914 (3) Job dispatched +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:09,077 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:09,441 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,567 Building dependency shell command for dependency 'R' +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,567 Find dependency R version 3.1.2 +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,575 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2aebec36b910> (isnull? False) +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Building dependency shell command for dependency 'r-snow' +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Find dependency r-snow version 0.4_1 +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-11 15:38:09,576 Failed to resolve dependency on 'r-snow', ignoring +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Building dependency shell command for dependency 'bioconductor-camera' +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Find dependency bioconductor-camera version 1.44.0 +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-11 15:38:09,577 Failed to resolve dependency on 'bioconductor-camera', ignoring +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Building dependency shell command for dependency 'r-batch' +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Find dependency r-batch version 1.1_4 +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,578 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,578 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,578 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) +galaxy.tools.deps WARNING 2016-04-11 15:38:09,578 Failed to resolve dependency on 'r-batch', ignoring +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,578 Building dependency shell command for dependency 'graphicsmagick' +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,578 Find dependency graphicsmagick version 1.3.20 +galaxy.tools.deps DEBUG 2016-04-11 15:38:09,578 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2aebec1cd390> (isnull? False) +galaxy.jobs.command_factory INFO 2016-04-11 15:38:09,656 Built script [/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/713334.1.short.q/tmpsEEpi3/deps/R/3.1.2/mmonsoor/camera_combinexsannos/2591056df814; export PACKAGE_BASE; . /tmp/713334.1.short.q/tmpsEEpi3/deps/R/3.1.2/mmonsoor/camera_combinexsannos/2591056df814/env.sh; PACKAGE_BASE=/tmp/713334.1.short.q/tmpsEEpi3/deps/graphicsmagick/1.3.20/mmonsoor/camera_combinexsannos/2591056df814; export PACKAGE_BASE; . /tmp/713334.1.short.q/tmpsEEpi3/deps/graphicsmagick/1.3.20/mmonsoor/camera_combinexsannos/2591056df814/env.sh; LANG=C Rscript /tmp/713334.1.short.q/tmpsEEpi3/shed_tools/testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/2591056df814/camera_combinexsannos/CAMERA.r xfunction combinexsAnnos image_pos /tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_1.dat image_neg /tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_2.dat variableMetadataOutput /tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_3.dat pos TRUE tol 2 ruleset 1,1 convert_param FALSE keep_meta TRUE] +galaxy.jobs.runners DEBUG 2016-04-11 15:38:09,912 (3) command is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/tool_script.sh; return_code=$?; python "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/set_metadata_3_tNOM.py" "/tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/galaxy.json" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_3_58fsJC,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_y6cHAM,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_3_K7CNlc,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_3_EMb9Bo,/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_3.dat,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_3_fy9km1" 5242880; sh -c "exit $return_code" +galaxy.jobs.runners.local DEBUG 2016-04-11 15:38:09,929 (3) executing job script: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/galaxy_3.sh +galaxy.jobs DEBUG 2016-04-11 15:38:09,940 (3) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:10,244 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:10,411 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:12,015 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:12,198 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +galaxy.jobs.runners.local DEBUG 2016-04-11 15:38:12,523 execution finished: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/galaxy_3.sh +galaxy.jobs.output_checker INFO 2016-04-11 15:38:12,566 Job 3: Fatal error: Exit code 1 () +galaxy.jobs.output_checker DEBUG 2016-04-11 15:38:12,566 Tool exit code indicates an error, failing job. +galaxy.jobs DEBUG 2016-04-11 15:38:12,633 (3) setting dataset 3 state to ERROR +galaxy.jobs DEBUG 2016-04-11 15:38:13,010 job 3 ended (finish() executed in (486.830 ms)) +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:15,404 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:15,554 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:15,556 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:15,612 "GET /api/histories/2891970512fa2d5a/contents?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:15,614 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:15,781 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:15,783 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:15,896 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:15,898 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:16,277 "GET /api/jobs/54f2a3a23292eb07?full=true&key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:16,279 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:16,432 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:16,434 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:16,485 "GET /api/histories/2891970512fa2d5a/contents?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:16,487 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:16,647 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:16,649 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:16,760 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None +functional_tests.py INFO 2016-04-11 15:38:16,989 Shutting down +functional_tests.py INFO 2016-04-11 15:38:16,989 Shutting down embedded web server +functional_tests.py INFO 2016-04-11 15:38:16,992 Embedded web server stopped +functional_tests.py INFO 2016-04-11 15:38:16,992 Shutting down app +galaxy.jobs.handler INFO 2016-04-11 15:38:16,992 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-11 15:38:16,992 job handler queue stopped +galaxy.jobs.runners INFO 2016-04-11 15:38:16,992 TaskRunner: Sending stop signal to 2 worker threads +galaxy.jobs.runners INFO 2016-04-11 15:38:16,992 LocalRunner: Sending stop signal to 5 worker threads +galaxy.jobs.handler INFO 2016-04-11 15:38:16,993 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-11 15:38:16,993 job handler stop queue stopped +functional_tests.py INFO 2016-04-11 15:38:16,994 Embedded Universe application stopped +functional_tests.py INFO 2016-04-11 15:38:16,994 Cleaning up temporary files in /tmp/713334.1.short.q/tmpi0htl5/tmpWnIGuv +galaxy.jobs.handler INFO 2016-04-11 15:38:17,651 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-11 15:38:17,652 job handler queue stopped +galaxy.jobs.runners INFO 2016-04-11 15:38:17,652 TaskRunner: Sending stop signal to 2 worker threads +galaxy.jobs.runners INFO 2016-04-11 15:38:17,652 LocalRunner: Sending stop signal to 5 worker threads +galaxy.jobs.handler INFO 2016-04-11 15:38:17,652 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-11 15:38:17,652 job handler stop queue stopped +testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3[0]: failed +testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3[0]: failed