Mercurial > repos > lecorguille > camera_annotate
diff qsub.err @ 12:db270f704d93 draft
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835-dirty
| author | lecorguille |
|---|---|
| date | Thu, 14 Apr 2016 11:00:27 -0400 |
| parents | d33e0ed5f32a |
| children | ba7db5b70639 |
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--- a/qsub.err Thu Apr 14 10:03:48 2016 -0400 +++ b/qsub.err Thu Apr 14 11:00:27 2016 -0400 @@ -20,1112 +20,25 @@ 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 +DEBUG:galaxy.app:python path is: /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/lib, /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/lib, /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/test, /tmp/714419.1.short.q/tmp6zzhM3/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 +CAMERA.annotate ( testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 ) > Test-1 ... ERROR ====================================================================== -FAIL: CAMERA.annotate ( testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 ) > Test-1 +ERROR: CAMERA.annotate ( testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): - File "/tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/test/functional/test_toolbox.py", line 289, in test_tool + File "/tmp/714419.1.short.q/tmp6zzhM3/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 << ---------------------- + File "/tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/test/functional/test_toolbox.py", line 38, in do_it + stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) + File "/tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/test/base/interactor.py", line 40, in stage_data_in_history + upload_wait = galaxy_interactor.stage_data_async( test_data, history, shed_tool_id ) + File "/tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/test/base/interactor.py", line 174, in stage_data_async + "files_0|file_data": open( file_name, 'rb') +IOError: [Errno 2] No such file or directory: u'/tmp/714419.1.short.q/tmp6zzhM3/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/d33e0ed5f32a/camera_annotate/test-data/sacuri_dir_root.zip' -------------------- >> 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 @@ -1139,197 +52,126 @@ 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: DEBUG: Validated and populated state for tool request (26.178 ms) +galaxy.tools.actions.upload: DEBUG: Persisted uploads (29.632 ms) +galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (450.856 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) +galaxy.tools.actions.upload: DEBUG: Created upload job (229.375 ms) +galaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (710.457 ms) +galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (759.156 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: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 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 +galaxy.jobs: DEBUG: (1) Working directory for job is: /tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1 +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 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.runners: DEBUG: Job [1] queued (204.971 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: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 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: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) +galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring +galaxy.jobs.command_factory: INFO: Built script [/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/tools/data_source/upload.py /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev /tmp/714419.1.short.q/tmp6zzhM3/tmp/tmpjP3KUB /tmp/714419.1.short.q/tmp6zzhM3/tmp/tmpNZ2o6u 1:/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/dataset_1_files:/tmp/714419.1.short.q/tmp6zzhM3/files/000/dataset_1.dat] +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 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 -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: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners: DEBUG: (1) command is: /tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/set_metadata_MqaJuZ.py" "/tmp/714419.1.short.q/tmp6zzhM3/tmp/tmpjP3KUB" "/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/galaxy.json" "/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_GavpWf,/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_X9MeXX,/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_SKjWPt,/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_WKXGCU,/tmp/714419.1.short.q/tmp6zzhM3/files/000/dataset_1.dat,/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_48OdEJ" 5242880; sh -c "exit $return_code" +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +galaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/galaxy_1.sh +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs: DEBUG: (1) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 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=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost +galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/galaxy_1.sh +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 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 ${GALAXY_SLOTS:-1} sigma 6 perfwhm 0.6 maxcharge 3 maxiso 4 minfrac 0.5 ppm 5 mzabs 0.015 intval into max_peaks 100 quick FALSE polarity negative cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE multiplier 3 runDiffreport TRUE eicmax 200 eicwidth 200 value into sortpval FALSE h 480 w 640 mzdec 2 new_file_path /tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_] -requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost -galaxy.jobs.runners: DEBUG: (2) command is: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/tool_script.sh; return_code=$?; 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 +requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None --------------------- >> end captured logging << --------------------- ---------------------------------------------------------------------- -XML: /tmp/714401.1.short.q/tmpAQxCGj/xunit.xml +XML: /tmp/714419.1.short.q/tmp6zzhM3/xunit.xml ---------------------------------------------------------------------- -Ran 1 test in 40.033s +Ran 1 test in 8.920s -FAILED (failures=1) -cp: cannot stat `/tmp/714401.1.short.q/tmpAQxCGj/jobfiles/*': No such file or directory +FAILED (errors=1) +cp: cannot stat `/tmp/714419.1.short.q/tmp6zzhM3/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.