Mercurial > repos > lecorguille > camera_annotate
view qsub.err @ 13:ba7db5b70639 draft
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
| author | lecorguille |
|---|---|
| date | Sun, 17 Apr 2016 16:36:55 -0400 |
| parents | db270f704d93 |
| children |
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/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 /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/714467.1.short.q/tmpR_swdX/galaxy-dev/scripts, /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/lib, /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/lib, /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/test, /tmp/714467.1.short.q/tmpR_swdX/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/714467.1.short.q/tmpR_swdX/galaxy-dev/test/functional/test_toolbox.py", line 299, in test_tool self.do_it( td ) File "/tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/test/functional/test_toolbox.py", line 75, 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. -------------------------------------- | 3 - 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/714467.1.short.q/tmpR_swdX | 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/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.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/714467.1.short.q/tmpR_swdX/tmp/primary_6_ | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1566 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 243 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | Error in getAllPeakEICs(object, index = index) : | Raw data file:sacuri/bio/HU_neg_017.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 4 - 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/714467.1.short.q/tmpR_swdX | 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/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.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/714467.1.short.q/tmpR_swdX/tmp/primary_6_ | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1566 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 243 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | Error in getAllPeakEICs(object, index = index) : | Raw data file:sacuri/bio/HU_neg_017.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 5 - 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/714467.1.short.q/tmpR_swdX | 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/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.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/714467.1.short.q/tmpR_swdX/tmp/primary_6_ | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1566 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 243 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | Error in getAllPeakEICs(object, index = index) : | Raw data file:sacuri/bio/HU_neg_017.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 6 - 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/714467.1.short.q/tmpR_swdX | 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/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.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/714467.1.short.q/tmpR_swdX/tmp/primary_6_ | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1566 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 243 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | Error in getAllPeakEICs(object, index = index) : | Raw data file:sacuri/bio/HU_neg_017.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- History with id 2891970512fa2d5a in error - summary of datasets in error below. -------------------------------------- | 3 - 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/714467.1.short.q/tmpR_swdX | 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/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.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/714467.1.short.q/tmpR_swdX/tmp/primary_6_ | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1566 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 243 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | Error in getAllPeakEICs(object, index = index) : | Raw data file:sacuri/bio/HU_neg_017.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 4 - 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/714467.1.short.q/tmpR_swdX | 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/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.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/714467.1.short.q/tmpR_swdX/tmp/primary_6_ | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1566 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 243 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | Error in getAllPeakEICs(object, index = index) : | Raw data file:sacuri/bio/HU_neg_017.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 5 - 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/714467.1.short.q/tmpR_swdX | 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/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.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/714467.1.short.q/tmpR_swdX/tmp/primary_6_ | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1566 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 243 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | Error in getAllPeakEICs(object, index = index) : | Raw data file:sacuri/bio/HU_neg_017.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 6 - 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/714467.1.short.q/tmpR_swdX | 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/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.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/714467.1.short.q/tmpR_swdX/tmp/primary_6_ | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1566 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 243 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | Error in getAllPeakEICs(object, index = index) : | Raw data file:sacuri/bio/HU_neg_017.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- History with id 2891970512fa2d5a in error - summary of datasets in error below. -------------------------------------- | 3 - 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/714467.1.short.q/tmpR_swdX | 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/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.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/714467.1.short.q/tmpR_swdX/tmp/primary_6_ | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1566 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 243 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | Error in getAllPeakEICs(object, index = index) : | Raw data file:sacuri/bio/HU_neg_017.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 4 - 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/714467.1.short.q/tmpR_swdX | 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/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.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/714467.1.short.q/tmpR_swdX/tmp/primary_6_ | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1566 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 243 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | Error in getAllPeakEICs(object, index = index) : | Raw data file:sacuri/bio/HU_neg_017.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 5 - 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/714467.1.short.q/tmpR_swdX | 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/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.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/714467.1.short.q/tmpR_swdX/tmp/primary_6_ | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1566 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 243 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | Error in getAllPeakEICs(object, index = index) : | Raw data file:sacuri/bio/HU_neg_017.mzXML not found ! | Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs | Execution halted | -------------------------------------- | 6 - 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/714467.1.short.q/tmpR_swdX | 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/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat | variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat | dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat | xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.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/714467.1.short.q/tmpR_swdX/tmp/primary_6_ | zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat | INFILE PROCESSING INFO | ARGUMENTS PROCESSING INFO | MAIN PROCESSING INFO | Start grouping after retention time. | Created 1566 pseudospectra. | Generating peak matrix! | Run isotope peak annotation | % finished: 10 20 30 40 50 60 70 80 90 100 | Found isotopes: 243 | Start grouping after correlation. | Generating EIC's .. | Dataset Job Standard Error: | Fatal error: Exit code 1 () | Error in getAllPeakEICs(object, index = index) : | Raw data file:sacuri/bio/HU_neg_017.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 (47.490 ms) galaxy.tools.actions.upload: DEBUG: Persisted uploads (20.544 ms) galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (391.258 ms) galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1 galaxy.tools.actions.upload: DEBUG: Created upload job (273.829 ms) galaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (686.205 ms) galaxy.tools.execute: DEBUG: Executed 1 job(s) for tool upload1 request: (727.583 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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/714467.1.short.q/tmpR_swdX/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=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners: DEBUG: Job [1] queued (154.781 ms) galaxy.jobs.handler: INFO: (1) Job dispatched requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.command_factory: INFO: Built script [/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/tools/data_source/upload.py /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev /tmp/714467.1.short.q/tmpR_swdX/tmp/tmpK4jM7r /tmp/714467.1.short.q/tmpR_swdX/tmp/tmpyH3qpG 1:/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/dataset_1_files:/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat] requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners: DEBUG: (1) command is: mkdir -p working; cd working; /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/tool_script.sh; return_code=$?; cd ..; python "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/set_metadata_eD8s7d.py" "/tmp/714467.1.short.q/tmpR_swdX/tmp/tmpK4jM7r" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/working/galaxy.json" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_jShRti,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_oFrnPD,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_BhnvZW,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_Een9yT,/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_R_kK3g" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/714467.1.short.q/tmpR_swdX/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=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/1/galaxy_1.sh requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.model.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 1 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs: DEBUG: job 1 ended (finish() executed in (836.273 ms)) galaxy.tools: DEBUG: Validated and populated state for tool request (44.879 ms) galaxy.tools.actions.upload: DEBUG: Persisted uploads (20.644 ms) galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (508.110 ms) galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 2 galaxy.tools.actions.upload: DEBUG: Created upload job (216.184 ms) galaxy.tools.execute: DEBUG: Tool [upload1] created job [2] (745.459 ms) galaxy.tools.execute: DEBUG: Executed 1 job(s) for tool upload1 request: (787.748 ms) galaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2 requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.handler: DEBUG: (2) Dispatching to local runner galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners: DEBUG: Job [2] queued (142.382 ms) galaxy.jobs.handler: INFO: (2) Job dispatched requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.command_factory: INFO: Built script [/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/tool_script.sh] for tool command[python /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev/tools/data_source/upload.py /tmp/714467.1.short.q/tmpR_swdX/galaxy-dev /tmp/714467.1.short.q/tmpR_swdX/tmp/tmpK4jM7r /tmp/714467.1.short.q/tmpR_swdX/tmp/tmpxnh06b 2:/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/dataset_2_files:/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat] requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners: DEBUG: (2) command is: mkdir -p working; cd working; /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/tool_script.sh; return_code=$?; cd ..; python "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/set_metadata_s1bC30.py" "/tmp/714467.1.short.q/tmpR_swdX/tmp/tmpK4jM7r" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/working/galaxy.json" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_4VZIsA,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_8kyCYN,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_Wr01BS,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_8aeiqq,/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2__DjwYh" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/galaxy_2.sh galaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/2/galaxy_2.sh requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.model.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 2 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=8429373991935695d3155e6b5342eb99 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 (73.689 ms) galaxy.tools.actions: INFO: Handled output named variableMetadata for tool testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 (110.026 ms) galaxy.jobs: DEBUG: job 2 ended (finish() executed in (767.672 ms)) galaxy.tools.actions: INFO: Handled output named datamatrix for tool testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 (138.821 ms) galaxy.tools.actions: INFO: Handled output named rdata for tool testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 (94.946 ms) galaxy.tools.actions: INFO: Handled output named output_diffreport for tool testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 (109.181 ms) galaxy.tools.actions: INFO: Added output datasets to history (62.241 ms) galaxy.tools.actions: INFO: Verified access to datasets for Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] (25.832 ms) galaxy.tools.actions: INFO: Setup for job Job[unflushed,tool_id=testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] complete, ready to flush (70.198 ms) galaxy.tools.actions: INFO: Flushed transaction for job Job[id=3,tool_id=testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] (98.006 ms) galaxy.tools.execute: DEBUG: Tool [testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] created job [3] (695.936 ms) galaxy.tools.execute: DEBUG: Executed 1 job(s) for tool testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 request: (734.968 ms) requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs: DEBUG: (3) Working directory for job is: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3 galaxy.jobs.handler: DEBUG: (3) Dispatching to local runner requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None galaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///) galaxy.jobs.runners: DEBUG: Job [3] queued (127.546 ms) galaxy.jobs.handler: INFO: (3) Job dispatched requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost 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 0x2b67c021cd90> (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 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (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 0x2b67c021cd10> (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 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (isnull? True) galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47e2dd0> (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 0x2b67c021cf10> (isnull? False) requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None galaxy.jobs.command_factory: INFO: Built script [/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/714467.1.short.q/tmpR_swdX/deps/R/3.1.2/lecorguille/camera_annotate/db270f704d93; export PACKAGE_BASE; . /tmp/714467.1.short.q/tmpR_swdX/deps/R/3.1.2/lecorguille/camera_annotate/db270f704d93/env.sh; PACKAGE_BASE=/tmp/714467.1.short.q/tmpR_swdX/deps/bioconductor-camera/1.22.0/lecorguille/camera_annotate/db270f704d93; export PACKAGE_BASE; . /tmp/714467.1.short.q/tmpR_swdX/deps/bioconductor-camera/1.22.0/lecorguille/camera_annotate/db270f704d93/env.sh; PACKAGE_BASE=/tmp/714467.1.short.q/tmpR_swdX/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/db270f704d93; export PACKAGE_BASE; . /tmp/714467.1.short.q/tmpR_swdX/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/db270f704d93/env.sh; LANG=C Rscript /tmp/714467.1.short.q/tmpR_swdX/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/db270f704d93/camera_annotate/CAMERA.r xfunction annotatediff image /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_1.dat variableMetadataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat dataMatrixOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat xsetRdataOutput /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat convert_param FALSE num_digits 0 nSlaves ${GALAXY_SLOTS:-1} sigma 6 perfwhm 0.6 maxcharge 3 maxiso 4 minfrac 0.5 ppm 5 mzabs 0.015 intval into max_peaks 100 quick FALSE polarity negative cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE multiplier 3 runDiffreport TRUE eicmax 200 eicwidth 200 value into sortpval FALSE h 480 w 640 mzdec 2 new_file_path /tmp/714467.1.short.q/tmpR_swdX/tmp/primary_6_ zipfile /tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_2.dat] requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None galaxy.jobs.runners: DEBUG: (3) command is: mkdir -p working; cd working; /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/tool_script.sh; return_code=$?; cd ..; python "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/set_metadata_Xzws5e.py" "/tmp/714467.1.short.q/tmpR_swdX/tmp/tmpK4jM7r" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/working/galaxy.json" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_3_cUhbAk,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_32gPgn,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_3_dAG7BN,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_3_wm2Akf,/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_3.dat,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_3_aw4Xwc" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_4_YmkXG2,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_4_M9NNV9,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_4_FSIoJm,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_4_rc0u_S,/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_4.dat,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_4_RAjtyp" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_5_2db6tk,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_5_MSmEkX,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_5_WtSkOw,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_5_zt5c5k,/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_5.dat,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_5_n4DVAW" "/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_6_wxbF7c,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_6_HXczlo,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_6_U8R0i3,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_6_ZxcRT0,/tmp/714467.1.short.q/tmpR_swdX/files/000/dataset_6.dat,/tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_6_Kf06sK" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local: DEBUG: (3) executing job script: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/galaxy_3.sh galaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/714467.1.short.q/tmpR_swdX/job_working_directory/000/3/galaxy_3.sh galaxy.jobs.output_checker: INFO: Job 3: Fatal error: Exit code 1 () galaxy.jobs.output_checker: DEBUG: Tool exit code indicates an error, failing job. galaxy.jobs: DEBUG: (3) setting dataset 3 state to ERROR galaxy.jobs: DEBUG: (3) setting dataset 4 state to ERROR galaxy.jobs: DEBUG: (3) setting dataset 5 state to ERROR galaxy.jobs: DEBUG: (3) setting dataset 6 state to ERROR galaxy.jobs: DEBUG: job 3 ended (finish() executed in (632.872 ms)) requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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/fa6d20d0fb68383f?key=8429373991935695d3155e6b5342eb99 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/fa6d20d0fb68383f/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?full=true&key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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/fa6d20d0fb68383f?key=8429373991935695d3155e6b5342eb99 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/fa6d20d0fb68383f/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/54f2a3a23292eb07?key=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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=8429373991935695d3155e6b5342eb99 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/fa6d20d0fb68383f?key=8429373991935695d3155e6b5342eb99 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/fa6d20d0fb68383f/provenance?key=8429373991935695d3155e6b5342eb99 HTTP/1.1" 200 None --------------------- >> end captured logging << --------------------- ---------------------------------------------------------------------- XML: /tmp/714467.1.short.q/tmpR_swdX/xunit.xml ---------------------------------------------------------------------- Ran 1 test in 123.315s FAILED (failures=1) cp: cannot stat `/tmp/714467.1.short.q/tmpR_swdX/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.