Mercurial > repos > lecorguille > camera_annotate
view qsub.err @ 11:d33e0ed5f32a draft
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835-dirty
| author | lecorguille |
|---|---|
| date | Thu, 14 Apr 2016 10:03:48 -0400 |
| parents | 01a900f2e464 |
| children | db270f704d93 |
line wrap: on
line source
/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/714401.1.short.q/tmpAQxCGj/galaxy-dev/lib, /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/lib, /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/test, /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python27.zip, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/plat-linux2, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-old, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-dynload, /opt/6.x/python-2.7.2/lib/python2.7, /opt/6.x/python-2.7.2/lib/python2.7/plat-linux2, /opt/6.x/python-2.7.2/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages INFO:galaxy.config:Logging at '10' level to 'stdout' /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:565: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. 'storage.' % (dialect.name, dialect.driver)) CAMERA.annotate ( testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 ) > Test-1 ... FAIL ====================================================================== FAIL: CAMERA.annotate ( testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/test/functional/test_toolbox.py", line 289, in test_tool self.do_it( td ) File "/tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/test/functional/test_toolbox.py", line 73, in do_it raise e JobOutputsError: Job in error state. Job in error state. Job in error state. -------------------- >> begin captured stdout << --------------------- History with id 2891970512fa2d5a in error - summary of datasets in error below. -------------------------------------- | 2 - xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv (HID - NAME) | Dataset Blurb: | error | Dataset Info: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj | Dataset Job Standard Output: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat | variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat | dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat | xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat | convert_param FALSE | num_digits 0 | nSlaves 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/714401.1.short.q/tmpAQxCGj/tmp/primary_5_ | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1336 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 167 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | arguments 'minimized' and 'invisible' are for Windows only | Error in getAllPeakEICs(object, index = index) : | Raw data file:./sacuri/bio/HU_neg_028.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 3 - xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv (HID - NAME) | Dataset Blurb: | error | Dataset Info: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj | Dataset Job Standard Output: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat | variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat | dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat | xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat | convert_param FALSE | num_digits 0 | nSlaves 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/714401.1.short.q/tmpAQxCGj/tmp/primary_5_ | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1336 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 167 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | arguments 'minimized' and 'invisible' are for Windows only | Error in getAllPeakEICs(object, index = index) : | Raw data file:./sacuri/bio/HU_neg_028.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 4 - xset.group.retcor.group.fillPeaks.annotate.negative.Rdata (HID - NAME) | Dataset Blurb: | error | Dataset Info: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj | Dataset Job Standard Output: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat | variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat | dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat | xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat | convert_param FALSE | num_digits 0 | nSlaves 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/714401.1.short.q/tmpAQxCGj/tmp/primary_5_ | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1336 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 167 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | arguments 'minimized' and 'invisible' are for Windows only | Error in getAllPeakEICs(object, index = index) : | Raw data file:./sacuri/bio/HU_neg_028.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 5 - xset.group.retcor.group.fillPeaks.annotateDiffreport (HID - NAME) | Dataset Blurb: | error | Dataset Info: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj | Dataset Job Standard Output: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat | variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat | dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat | xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat | convert_param FALSE | num_digits 0 | nSlaves 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/714401.1.short.q/tmpAQxCGj/tmp/primary_5_ | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1336 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 167 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | arguments 'minimized' and 'invisible' are for Windows only | Error in getAllPeakEICs(object, index = index) : | Raw data file:./sacuri/bio/HU_neg_028.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- History with id 2891970512fa2d5a in error - summary of datasets in error below. -------------------------------------- | 2 - xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv (HID - NAME) | Dataset Blurb: | error | Dataset Info: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj | Dataset Job Standard Output: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat | variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat | dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat | xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat | convert_param FALSE | num_digits 0 | nSlaves 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/714401.1.short.q/tmpAQxCGj/tmp/primary_5_ | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1336 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 167 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | arguments 'minimized' and 'invisible' are for Windows only | Error in getAllPeakEICs(object, index = index) : | Raw data file:./sacuri/bio/HU_neg_028.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 3 - xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv (HID - NAME) | Dataset Blurb: | error | Dataset Info: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj | Dataset Job Standard Output: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat | variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat | dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat | xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat | convert_param FALSE | num_digits 0 | nSlaves 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/714401.1.short.q/tmpAQxCGj/tmp/primary_5_ | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1336 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 167 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | arguments 'minimized' and 'invisible' are for Windows only | Error in getAllPeakEICs(object, index = index) : | Raw data file:./sacuri/bio/HU_neg_028.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 4 - xset.group.retcor.group.fillPeaks.annotate.negative.Rdata (HID - NAME) | Dataset Blurb: | error | Dataset Info: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj | Dataset Job Standard Output: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat | variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat | dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat | xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat | convert_param FALSE | num_digits 0 | nSlaves 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/714401.1.short.q/tmpAQxCGj/tmp/primary_5_ | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1336 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 167 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | arguments 'minimized' and 'invisible' are for Windows only | Error in getAllPeakEICs(object, index = index) : | Raw data file:./sacuri/bio/HU_neg_028.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 5 - xset.group.retcor.group.fillPeaks.annotateDiffreport (HID - NAME) | Dataset Blurb: | error | Dataset Info: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj | Dataset Job Standard Output: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat | variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat | dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat | xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat | convert_param FALSE | num_digits 0 | nSlaves 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/714401.1.short.q/tmpAQxCGj/tmp/primary_5_ | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1336 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 167 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | arguments 'minimized' and 'invisible' are for Windows only | Error in getAllPeakEICs(object, index = index) : | Raw data file:./sacuri/bio/HU_neg_028.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- History with id 2891970512fa2d5a in error - summary of datasets in error below. -------------------------------------- | 2 - xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv (HID - NAME) | Dataset Blurb: | error | Dataset Info: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj | Dataset Job Standard Output: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat | variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat | dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat | xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat | convert_param FALSE | num_digits 0 | nSlaves 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/714401.1.short.q/tmpAQxCGj/tmp/primary_5_ | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1336 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 167 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | arguments 'minimized' and 'invisible' are for Windows only | Error in getAllPeakEICs(object, index = index) : | Raw data file:./sacuri/bio/HU_neg_028.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 3 - xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv (HID - NAME) | Dataset Blurb: | error | Dataset Info: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj | Dataset Job Standard Output: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat | variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat | dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat | xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat | convert_param FALSE | num_digits 0 | nSlaves 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/714401.1.short.q/tmpAQxCGj/tmp/primary_5_ | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1336 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 167 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | arguments 'minimized' and 'invisible' are for Windows only | Error in getAllPeakEICs(object, index = index) : | Raw data file:./sacuri/bio/HU_neg_028.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 4 - xset.group.retcor.group.fillPeaks.annotate.negative.Rdata (HID - NAME) | Dataset Blurb: | error | Dataset Info: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj | Dataset Job Standard Output: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat | variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat | dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat | xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat | convert_param FALSE | num_digits 0 | nSlaves 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/714401.1.short.q/tmpAQxCGj/tmp/primary_5_ | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1336 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 167 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | arguments 'minimized' and 'invisible' are for Windows only | Error in getAllPeakEICs(object, index = index) : | Raw data file:./sacuri/bio/HU_neg_028.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 5 - xset.group.retcor.group.fillPeaks.annotateDiffreport (HID - NAME) | Dataset Blurb: | error | Dataset Info: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj | Dataset Job Standard Output: | PACKAGE INFO | parallel 3.1.2 | BiocGenerics 0.14.0 | Biobase 2.28.0 | Rcpp 0.12.0 | mzR 2.2.2 | tcltk 3.1.2 | igraph 0.7.1 | xcms 1.44.0 | snow 0.3.13 | CAMERA 1.22.0 | multtest 2.22.0 | batch 1.1.4 | ARGUMENTS INFO | xfunction annotatediff | image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat | variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat | dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat | xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat | convert_param FALSE | num_digits 0 | nSlaves 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/714401.1.short.q/tmpAQxCGj/tmp/primary_5_ | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1336 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 167 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | arguments 'minimized' and 'invisible' are for Windows only | Error in getAllPeakEICs(object, index = index) : | Raw data file:./sacuri/bio/HU_neg_028.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- --------------------- >> end captured stdout << ---------------------- -------------------- >> 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 (19.760 ms) galaxy.tools.actions.upload: DEBUG: Persisted uploads (22.581 ms) galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (487.187 ms) galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1 galaxy.tools.actions.upload: DEBUG: Created upload job (242.417 ms) galaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (752.711 ms) galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (795.117 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=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 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/714401.1.short.q/tmpAQxCGj/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=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners: DEBUG: Job [1] queued (194.097 ms) galaxy.jobs.handler: INFO: (1) Job dispatched requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 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 0x47bf090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None galaxy.jobs.command_factory: INFO: Built script [/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/tools/data_source/upload.py /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev /tmp/714401.1.short.q/tmpAQxCGj/tmp/tmpLPOdzn /tmp/714401.1.short.q/tmpAQxCGj/tmp/tmp0jkGJc 1:/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/dataset_1_files:/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat] requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners: DEBUG: (1) command is: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/set_metadata_XVRZb9.py" "/tmp/714401.1.short.q/tmpAQxCGj/tmp/tmpLPOdzn" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/galaxy.json" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_2H7S7g,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_bwLNVA,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_jembhp,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_7Ch0tX,/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_lR53Ty" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/714401.1.short.q/tmpAQxCGj/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=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/galaxy_1.sh requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 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 (72.417 ms) galaxy.tools.actions: INFO: Handled output (99.542 ms) galaxy.jobs: DEBUG: job 1 ended (finish() executed in (1044.369 ms)) galaxy.tools.actions: INFO: Handled output (144.572 ms) galaxy.tools.actions: INFO: Handled output (90.577 ms) galaxy.tools.actions: INFO: Handled output (84.692 ms) galaxy.tools.actions: INFO: Verified access to datasets (7.993 ms) galaxy.tools.execute: DEBUG: Tool [testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] created job [2] (651.728 ms) galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (715.204 ms) requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None galaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/714401.1.short.q/tmpAQxCGj/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: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners: DEBUG: Job [2] queued (121.409 ms) galaxy.jobs.handler: INFO: (2) Job dispatched requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 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 0x2b7e7c239b10> (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 0x47bf090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (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 1.22.0 galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b7e7c268890> (isnull? False) 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 0x47bf090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (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 0x2b7ec80fead0> (isnull? False) requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.command_factory: INFO: Built script [/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/714401.1.short.q/tmpAQxCGj/deps/R/3.1.2/lecorguille/camera_annotate/01a900f2e464; export PACKAGE_BASE; . /tmp/714401.1.short.q/tmpAQxCGj/deps/R/3.1.2/lecorguille/camera_annotate/01a900f2e464/env.sh; PACKAGE_BASE=/tmp/714401.1.short.q/tmpAQxCGj/deps/bioconductor-camera/1.22.0/lecorguille/camera_annotate/01a900f2e464; export PACKAGE_BASE; . /tmp/714401.1.short.q/tmpAQxCGj/deps/bioconductor-camera/1.22.0/lecorguille/camera_annotate/01a900f2e464/env.sh; PACKAGE_BASE=/tmp/714401.1.short.q/tmpAQxCGj/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/01a900f2e464; export PACKAGE_BASE; . /tmp/714401.1.short.q/tmpAQxCGj/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/01a900f2e464/env.sh; LANG=C Rscript /tmp/714401.1.short.q/tmpAQxCGj/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/01a900f2e464/camera_annotate/CAMERA.r xfunction annotatediff image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat convert_param FALSE num_digits 0 nSlaves ${GALAXY_SLOTS:-1} sigma 6 perfwhm 0.6 maxcharge 3 maxiso 4 minfrac 0.5 ppm 5 mzabs 0.015 intval into max_peaks 100 quick FALSE polarity negative cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE multiplier 3 runDiffreport TRUE eicmax 200 eicwidth 200 value into sortpval FALSE h 480 w 640 mzdec 2 new_file_path /tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_] requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners: DEBUG: (2) command is: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/tool_script.sh; return_code=$?; python "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/set_metadata_nPFswU.py" "/tmp/714401.1.short.q/tmpAQxCGj/tmp/tmpLPOdzn" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/galaxy.json" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_bsNzU9,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_ktNnvu,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_6PXLPl,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_db7cVH,/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_7qIivj" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_3_j4Mjr6,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_3_ir7l9Z,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_3_SuHDrD,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_3_ruts7J,/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_3_jvOjlv" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_4_3zPwDY,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_4_2ztBlR,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_4_jkuI4N,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_4_ADypZO,/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_4_xI2Wdp" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_5_ASl36X,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_5_QmXDdz,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_5_I6RNNV,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_5_SGtGLd,/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_5.dat,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_5_V21r1c" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/714401.1.short.q/tmpAQxCGj/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/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/galaxy_2.sh galaxy.jobs.output_checker: INFO: Job 2: Fatal error: Exit code 1 () galaxy.jobs.output_checker: DEBUG: Tool exit code indicates an error, failing job. galaxy.jobs: DEBUG: (2) setting dataset 2 state to ERROR galaxy.jobs: DEBUG: (2) setting dataset 3 state to ERROR galaxy.jobs: DEBUG: (2) setting dataset 4 state to ERROR galaxy.jobs: DEBUG: (2) setting dataset 5 state to ERROR galaxy.jobs: DEBUG: job 2 ended (finish() executed in (650.423 ms)) requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?full=true&key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 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=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None --------------------- >> end captured logging << --------------------- ---------------------------------------------------------------------- XML: /tmp/714401.1.short.q/tmpAQxCGj/xunit.xml ---------------------------------------------------------------------- Ran 1 test in 40.033s FAILED (failures=1) cp: cannot stat `/tmp/714401.1.short.q/tmpAQxCGj/jobfiles/*': No such file or directory There were problems with 1 test(s) - out of 1 test(s) executed. See /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.html for detailed breakdown.