Mercurial > repos > lecorguille > camera_annotate

comparison qsub.err @ 10:01a900f2e464 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
author lecorguille
date Tue, 12 Apr 2016 04:11:58 -0400
parents
children d33e0ed5f32a
comparison
equal deleted inserted replaced
9:c02d80efba80 10:01a900f2e464
1 /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.
2 SNIMissingWarning
3 /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.
4 InsecurePlatformWarning
5 You are using pip version 8.0.2+gx2, however version 8.1.1 is available.
6 You should consider upgrading via the 'pip install --upgrade pip' command.
7 You are using pip version 8.0.2+gx2, however version 8.1.1 is available.
8 You should consider upgrading via the 'pip install --upgrade pip' command.
9 /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.
10 SNIMissingWarning
11 /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.
12 InsecurePlatformWarning
13 You are using pip version 8.0.2+gx2, however version 8.1.1 is available.
14 You should consider upgrading via the 'pip install --upgrade pip' command.
15 /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.
16 SNIMissingWarning
17 /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.
18 InsecurePlatformWarning
19 You are using pip version 8.0.2+gx2, however version 8.1.1 is available.
20 You should consider upgrading via the 'pip install --upgrade pip' command.
21 You are using pip version 8.0.2+gx2, however version 8.1.1 is available.
22 You should consider upgrading via the 'pip install --upgrade pip' command.
23 DEBUG:galaxy.app:python path is: /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/lib, /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/lib, /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/test, /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python27.zip, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/plat-linux2, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-old, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-dynload, /opt/6.x/python-2.7.2/lib/python2.7, /opt/6.x/python-2.7.2/lib/python2.7/plat-linux2, /opt/6.x/python-2.7.2/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages
24 INFO:galaxy.config:Logging at '10' level to 'stdout'
25 /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.
26 'storage.' % (dialect.name, dialect.driver))
27 CAMERA.annotate ( testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 ) > Test-1 ... ERROR
28
29 ======================================================================
30 ERROR: CAMERA.annotate ( testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 ) > Test-1
31 ----------------------------------------------------------------------
32 Traceback (most recent call last):
33 File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/case.py", line 133, in run
34 self.runTest(result)
35 File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/case.py", line 151, in runTest
36 test(result)
37 File "/opt/6.x/python-2.7.2/lib/python2.7/unittest/case.py", line 391, in __call__
38 return self.run(*args, **kwds)
39 File "/opt/6.x/python-2.7.2/lib/python2.7/unittest/case.py", line 331, in run
40 result.addFailure(self, sys.exc_info())
41 File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/proxy.py", line 146, in addFailure
42 plugins.addFailure(self.test, err)
43 File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/plugins/manager.py", line 99, in __call__
44 return self.call(*arg, **kw)
45 File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/plugins/manager.py", line 167, in simple
46 result = meth(*arg, **kw)
47 File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nosehtml/plugin.py", line 93, in addFailure
48 self.print_test( 'failure', test, '\n'.join( traceback.format_exception( *error ) ) )
49 File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nosehtml/plugin.py", line 67, in print_test
50 print >> f.file, "<div id='capture_%d' style='display: none'><pre class='capture'>%s</pre></div>" % ( f.counter, cgi.escape( test.capturedOutput ) )
51 UnicodeEncodeError: 'ascii' codec can't encode character u'\u2018' in position 413: ordinal not in range(128)
52 -------------------- >> begin captured logging << --------------------
53 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
54 galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key
55 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/users?key=test_key HTTP/1.1" 200 None
56 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
57 galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key
58 requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users HTTP/1.1" 200 None
59 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
60 galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key
61 requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None
62 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
63 requests.packages.urllib3.connectionpool: DEBUG: "POST /api/histories HTTP/1.1" 200 None
64 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
65 galaxy.tools: DEBUG: Validated and populated state for tool request (18.524 ms)
66 galaxy.tools.actions.upload: DEBUG: Persisted uploads (20.819 ms)
67 galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (421.017 ms)
68 galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1
69 galaxy.tools.actions.upload: DEBUG: Created upload job (212.151 ms)
70 galaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (654.615 ms)
71 galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (699.689 ms)
72 requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None
73 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
74 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
75 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
76 galaxy.jobs: DEBUG: (1) Working directory for job is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1
77 galaxy.jobs.handler: DEBUG: (1) Dispatching to local runner
78 galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)
79 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
80 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
81 galaxy.jobs.runners: DEBUG: Job [1] queued (144.152 ms)
82 galaxy.jobs.handler: INFO: (1) Job dispatched
83 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
84 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
85 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
86 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
87 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools'
88 galaxy.tools.deps: DEBUG: Find dependency samtools version None
89 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
90 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
91 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
92 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
93 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
94 galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring
95 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
96 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
97 galaxy.jobs.command_factory: INFO: Built script [/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/tools/data_source/upload.py /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev /tmp/713417.1.short.q/tmp32I4oD/tmp/tmpIuu2Wr /tmp/713417.1.short.q/tmp32I4oD/tmp/tmpKio67E 1:/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/dataset_1_files:/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_1.dat]
98 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
99 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
100 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
101 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
102 galaxy.jobs.runners: DEBUG: (1) command is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/set_metadata_aCYbsb.py" "/tmp/713417.1.short.q/tmp32I4oD/tmp/tmpIuu2Wr" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/galaxy.json" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_XozciK,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_PCVo6A,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_POL2Ze,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_3vJ9WJ,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_1.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_hQCXbL" 5242880; sh -c "exit $return_code"
103 galaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/galaxy_1.sh
104 galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///)
105 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
106 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
107 galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/galaxy_1.sh
108 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
109 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
110 galaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 1
111 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
112 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
113 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
114 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
115 galaxy.tools: DEBUG: Validated and populated state for tool request (99.599 ms)
116 galaxy.jobs: DEBUG: job 1 ended (finish() executed in (864.203 ms))
117 galaxy.tools.actions: INFO: Handled output (134.928 ms)
118 galaxy.tools.actions: INFO: Handled output (71.983 ms)
119 galaxy.tools.actions: INFO: Handled output (90.651 ms)
120 galaxy.tools.actions: INFO: Handled output (90.794 ms)
121 galaxy.tools.actions: INFO: Verified access to datasets (8.282 ms)
122 galaxy.tools.execute: DEBUG: Tool [testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] created job [2] (601.149 ms)
123 galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (646.356 ms)
124 requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None
125 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
126 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
127 galaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2
128 galaxy.jobs.handler: DEBUG: (2) Dispatching to local runner
129 galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)
130 galaxy.jobs.runners: DEBUG: Job [2] queued (106.028 ms)
131 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
132 galaxy.jobs.handler: INFO: (2) Job dispatched
133 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
134 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'R'
135 galaxy.tools.deps: DEBUG: Find dependency R version 3.1.2
136 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2ac7e450d110> (isnull? False)
137 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'r-snow'
138 galaxy.tools.deps: DEBUG: Find dependency r-snow version 0.4_1
139 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
140 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
141 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
142 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
143 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
144 galaxy.tools.deps: WARNING: Failed to resolve dependency on 'r-snow', ignoring
145 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'bioconductor-camera'
146 galaxy.tools.deps: DEBUG: Find dependency bioconductor-camera version 1.44.0
147 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
148 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
149 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
150 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
151 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
152 galaxy.tools.deps: WARNING: Failed to resolve dependency on 'bioconductor-camera', ignoring
153 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'r-batch'
154 galaxy.tools.deps: DEBUG: Find dependency r-batch version 1.1_4
155 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
156 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
157 galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
158 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
159 galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
160 galaxy.tools.deps: WARNING: Failed to resolve dependency on 'r-batch', ignoring
161 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'graphicsmagick'
162 galaxy.tools.deps: DEBUG: Find dependency graphicsmagick version 1.3.20
163 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2ac83c0d9a50> (isnull? False)
164 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
165 galaxy.jobs.command_factory: INFO: Built script [/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/713417.1.short.q/tmp32I4oD/deps/R/3.1.2/lecorguille/camera_annotate/c02d80efba80; export PACKAGE_BASE; . /tmp/713417.1.short.q/tmp32I4oD/deps/R/3.1.2/lecorguille/camera_annotate/c02d80efba80/env.sh; PACKAGE_BASE=/tmp/713417.1.short.q/tmp32I4oD/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/c02d80efba80; export PACKAGE_BASE; . /tmp/713417.1.short.q/tmp32I4oD/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/c02d80efba80/env.sh; LANG=C Rscript /tmp/713417.1.short.q/tmp32I4oD/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/c02d80efba80/camera_annotate/CAMERA.r xfunction annotatediff image /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_1.dat variableMetadataOutput /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_2.dat dataMatrixOutput /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_3.dat xsetRdataOutput /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_4.dat convert_param FALSE num_digits 0 nSlaves ${GALAXY_SLOTS:-1} sigma 6 perfwhm 0.6 maxcharge 3 maxiso 4 minfrac 0.5 ppm 5 mzabs 0.015 intval into max_peaks 100 quick FALSE polarity negative cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE multiplier 3 runDiffreport TRUE eicmax 200 eicwidth 200 value into sortpval FALSE h 480 w 640 mzdec 2 new_file_path /tmp/713417.1.short.q/tmp32I4oD/tmp/primary_5_]
166 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
167 galaxy.jobs.runners: DEBUG: (2) command is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/tool_script.sh; return_code=$?; python "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/set_metadata_7oSiGt.py" "/tmp/713417.1.short.q/tmp32I4oD/tmp/tmpIuu2Wr" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/galaxy.json" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_yQypOr,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_5pYigd,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_dqnE6s,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_bb9G1l,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_2.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_qGNTro" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_3_GFPZBf,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_3_dzMzqz,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_3_YTXBdt,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_3_60vr5_,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_3.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_3_CF9v7P" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_4_dtyp5t,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_4_0jY9lR,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_4_IYAPP7,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_4_g18Jla,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_4.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_4_YPXaBQ" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_5_w61b96,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_5_oh73F9,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_5_jXk9Pn,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_5_GgatPH,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_5.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_5_lY8WCQ" 5242880; sh -c "exit $return_code"
168 galaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/galaxy_2.sh
169 galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)
170 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
171 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
172 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
173 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
174 galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/galaxy_2.sh
175 galaxy.jobs.output_checker: INFO: Job 2: Fatal error: Exit code 1 ()
176 galaxy.jobs.output_checker: DEBUG: Tool exit code indicates an error, failing job.
177 galaxy.jobs: DEBUG: (2) setting dataset 2 state to ERROR
178 galaxy.jobs: DEBUG: (2) setting dataset 3 state to ERROR
179 galaxy.jobs: DEBUG: (2) setting dataset 4 state to ERROR
180 galaxy.jobs: DEBUG: (2) setting dataset 5 state to ERROR
181 galaxy.jobs: DEBUG: job 2 ended (finish() executed in (651.127 ms))
182 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
183 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
184 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
185 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
186 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
187 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
188 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
189 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
190 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
191 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
192 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
193 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
194 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
195 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
196 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
197 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
198 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
199 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
200 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
201 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
202 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
203 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?full=true&key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
204 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
205 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
206 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
207 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
208 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
209 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
210 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
211 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
212 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
213 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
214 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
215 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
216 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
217 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
218 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
219 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
220 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
221 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
222 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
223 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
224 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
225 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
226 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
227 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
228 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
229 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
230 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
231 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
232 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
233 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
234 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
235 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
236 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
237 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
238 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
239 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
240 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
241 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
242 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
243 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
244 --------------------- >> end captured logging << ---------------------
245
246 ----------------------------------------------------------------------
247 XML: /tmp/713417.1.short.q/tmp32I4oD/xunit.xml
248 ----------------------------------------------------------------------
249 Ran 1 test in 20.783s
250
251 FAILED (errors=1)
252 cp: cannot stat `/tmp/713417.1.short.q/tmp32I4oD/jobfiles/*': No such file or directory
253 There were problems with 2 test(s) - out of 2 test(s) executed. See /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.html for detailed breakdown.