Mercurial > repos > lecorguille > camera_annotate
changeset 12:db270f704d93 draft
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835-dirty
| author | lecorguille |
|---|---|
| date | Thu, 14 Apr 2016 11:00:27 -0400 |
| parents | d33e0ed5f32a |
| children | ba7db5b70639 |
| files | qsub.err qsub.out test-data/sacuri_dir_root.zip test-data/xset.group.retcor.group.fillPeaks.annotate.negative.Rdata test-data/xset.group.retcor.group.fillPeaks.annotate.variableMetadata.Xdiffreport.zip |
| diffstat | 5 files changed, 1216 insertions(+), 2444 deletions(-) [+] |
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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.
--- a/qsub.out Thu Apr 14 10:03:48 2016 -0400 +++ b/qsub.out Thu Apr 14 11:00:27 2016 -0400 @@ -1,6 +1,6 @@ git --git-dir /home/fr2424/sib/lecorguille/.planemo/gx_repo fetch >/dev/null 2>&1 -cd /tmp/714401.1.short.q/tmpAQxCGj; git clone --branch 'master' '/home/fr2424/sib/lecorguille/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS} -Initialized empty Git repository in /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/.git/ +cd /tmp/714419.1.short.q/tmp6zzhM3; git clone --branch 'master' '/home/fr2424/sib/lecorguille/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS} +Initialized empty Git repository in /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/.git/ Set COMMON_STARTUP_ARGS to --dev-wheels Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample @@ -92,7 +92,7 @@ Requirement already satisfied (use --upgrade to upgrade): six>=1.9 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): pbr>=0.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): ordereddict in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from funcsigs>=1->mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) -Starting galaxy with command [cd /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/run.sh $COMMON_STARTUP_ARGS --daemon --wait] +Starting galaxy with command [cd /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/run.sh $COMMON_STARTUP_ARGS --daemon --wait] Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv Ignoring indexes: https://pypi.python.org/simple Requirement already up-to-date: pip==8.0.2+gx2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages @@ -139,10 +139,10 @@ Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv -............. +............... Installing repositories - this may take some time... -Testing using galaxy_root /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev -Testing tools with command [cd /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.html --xunit_report_file /tmp/714401.1.short.q/tmpAQxCGj/xunit.xml --structured_data_report_file /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.json -installed] +Testing using galaxy_root /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev +Testing tools with command [cd /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.html --xunit_report_file /tmp/714419.1.short.q/tmp6zzhM3/xunit.xml --structured_data_report_file /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.json -installed] Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv Ignoring indexes: https://pypi.python.org/simple Requirement already up-to-date: pip==8.0.2+gx2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages @@ -197,1177 +197,1107 @@ Requirement already satisfied (use --upgrade to upgrade): pbr>=0.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): ordereddict in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from funcsigs>=1->mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv -[('app:main', 'new_file_path', '/tmp/714401.1.short.q/tmpYE8cIL/tmpVeogQe/new_files_path_Zk6Uub'), ('app:main', 'database_connection', 'sqlite:////tmp/714401.1.short.q/tmpYE8cIL/tmpVeogQe/database/universe.sqlite'), ('app:main', 'data_manager_config_file', 'config/data_manager_conf.xml.sample,test/functional/tools/sample_data_manager_conf.xml'), ('app:main', 'job_queue_workers', 5), ('app:main', 'log_destination', 'stdout'), ('app:main', 'allow_user_deletion', True), ('app:main', 'master_api_key', 'test_key'), ('app:main', 'tool_config_file', '/tmp/714401.1.short.q/tmp3wnbXv'), ('app:main', 'template_cache_path', '/tmp/714401.1.short.q/tmpYE8cIL/tmpVeogQe/database/compiled_templates'), ('app:main', 'job_working_directory', '/tmp/714401.1.short.q/tmpYE8cIL/tmpVeogQe/job_working_directory_eYJfla'), ('app:main', 'tool_dependency_dir', '/tmp/714401.1.short.q/tmpAQxCGj/deps'), ('app:main', 'check_migrate_tools', False), ('app:main', 'tool_path', 'tools'), ('app:main', 'enable_beta_tool_formats', True), ('app:main', 'user_library_import_dir', None), ('app:main', 'galaxy_data_manager_data_path', '/tmp/714401.1.short.q/tmpYE8cIL/data_manager_test_tmpBMgb4s/data_manager_tool-dataFeK_yC'), ('app:main', 'tool_data_table_config_path', 'config/tool_data_table_conf.xml.sample,test/functional/tool-data/sample_tool_data_tables.xml'), ('app:main', 'file_path', '/tmp/714401.1.short.q/tmpYE8cIL/tmpVeogQe/database/files'), ('app:main', 'datatype_converters_config_file', 'datatype_converters_conf.xml.sample'), ('app:main', 'database_auto_migrate', True), ('app:main', 'use_tasked_jobs', True), ('app:main', 'auto_configure_logging', True), ('app:main', 'tool_parse_help', False), ('app:main', 'shed_tool_data_table_config', 'config/shed_tool_data_table_conf.xml'), ('app:main', 'update_integrated_tool_panel', False), ('app:main', 'admin_users', 'test@bx.psu.edu'), ('app:main', 'template_path', 'templates'), ('app:main', 'allow_user_creation', True), ('app:main', 'use_heartbeat', False), ('app:main', 'allow_library_path_paste', True), ('app:main', 'api_allow_run_as', 'test@bx.psu.edu'), ('app:main', 'test_conf', 'test.conf'), ('app:main', 'id_secret', 'changethisinproductiontoo'), ('app:main', 'library_import_dir', None), ('app:main', 'cleanup_job', 'onsuccess'), ('app:main', 'running_functional_tests', True)] -galaxy.queue_worker INFO 2016-04-14 15:51:10,770 Initalizing main Galaxy Queue Worker on sqlalchemy+sqlite:// -tool_shed.tool_shed_registry DEBUG 2016-04-14 15:51:10,811 Loading references to tool sheds from /tmp/714401.1.short.q/tmpAQxCGj/tool_sheds_conf.xml -tool_shed.tool_shed_registry DEBUG 2016-04-14 15:51:10,811 Loaded reference to tool shed: Target Shed -galaxy.app DEBUG 2016-04-14 15:51:10,812 Using "galaxy.ini" config file: /tmp/714401.1.short.q/tmpYE8cIL/functional_tests_wsgi.ini -migrate.versioning.repository DEBUG 2016-04-14 15:51:10,886 Loading repository lib/galaxy/model/migrate... -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,887 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,887 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully 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2016-04-14 15:51:10,904 Script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py loaded successfully -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py... -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Loading script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py... -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py loaded successfully -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Loading script lib/galaxy/model/migrate/versions/0119_job_metrics.py... -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Script lib/galaxy/model/migrate/versions/0119_job_metrics.py 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2016-04-14 15:51:10,905 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py... -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py... -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py... -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,906 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,906 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py... -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,906 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,906 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... -migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,906 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully -migrate.versioning.repository DEBUG 2016-04-14 15:51:10,906 Repository lib/galaxy/model/migrate loaded successfully -migrate.versioning.repository DEBUG 2016-04-14 15:51:10,906 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) -galaxy.config INFO 2016-04-14 15:51:10,960 Install database targetting Galaxy's database configuration. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:10,998 Loading datatypes from /tmp/714401.1.short.q/tmpAQxCGj/tmp/tmp-toolshed-acalpd1lhytY -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,003 Loading datatypes from /tmp/714401.1.short.q/tmpAQxCGj/tmp/tmp-toolshed-acalpdRs1z_c -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,003 Exception importing proprietary code file /tmp/714401.1.short.q/tmpAQxCGj/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/rdata_xcms_datatypes/bff835d58914/rdata_xcms_datatypes/binary: No module named binary -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,003 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,016 Loading datatypes from ./config/datatypes_conf.xml.sample -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,016 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,017 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,018 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,018 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,018 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,018 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,018 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,018 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,020 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,020 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,020 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,020 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,020 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,020 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,021 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,021 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,021 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,021 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,021 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,021 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,024 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,024 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,024 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,024 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,024 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,024 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,025 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,025 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,025 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,025 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,027 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,027 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,027 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,027 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,029 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,029 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,029 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,029 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,029 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,029 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,039 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,039 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,039 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,039 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,039 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,041 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,041 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,041 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,044 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,044 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,045 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,046 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,046 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,046 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,046 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,052 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,052 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,052 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,052 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,052 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,052 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,054 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,054 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,054 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,054 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,054 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,054 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,055 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,055 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,055 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,055 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,055 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,056 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,056 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,056 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,056 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,056 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,056 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,058 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,058 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,058 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,058 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,058 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,058 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,059 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,059 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,059 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,059 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,059 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,059 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,060 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,060 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,060 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,060 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,060 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,062 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,062 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,062 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,062 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,062 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,062 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,063 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,063 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,063 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Overriding conflicting datatype with extension 'rdata', using datatype from ./config/datatypes_conf.xml.sample. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,065 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,065 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,066 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,066 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,066 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,066 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,066 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:IdpDB' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:SQlite' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:H5' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Bam' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Sff' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Removed conflicting sniffer for datatype 'galaxy.datatypes.xml:GenericXml' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Maf' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Lav' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:csFasta' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fasta' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fastq' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Wiggle' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.images:Html' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Axt' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Bed' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gtf' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff3' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Pileup' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Interval' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Sam' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:CSV' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,078 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,078 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,078 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt -galaxy.jobs WARNING 2016-04-14 15:51:11,133 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/714401.1.short.q/tmpYE8cIL/functional_tests_wsgi.ini" instead -galaxy.jobs DEBUG 2016-04-14 15:51:11,133 Loading job configuration from /tmp/714401.1.short.q/tmpYE8cIL/functional_tests_wsgi.ini -galaxy.jobs DEBUG 2016-04-14 15:51:11,134 Done loading job configuration -beaker.container DEBUG 2016-04-14 15:51:11,157 data file /tmp/714401.1.short.q/tmpAQxCGj/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache -galaxy.tools.toolbox.watcher INFO 2016-04-14 15:51:11,158 Watchdog library unavailble, cannot monitor tools. -galaxy.tools.toolbox.base INFO 2016-04-14 15:51:11,158 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/tool_conf.xml -galaxy.tools.toolbox.base INFO 2016-04-14 15:51:11,169 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/config/shed_tool_conf.xml -galaxy.tools.toolbox.base INFO 2016-04-14 15:51:11,206 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/empty_tool_conf.xml -galaxy.tools.toolbox.base DEBUG 2016-04-14 15:51:11,206 Loaded tool id: upload1, version: 1.1.4 into tool panel.. -galaxy.tools.toolbox.base DEBUG 2016-04-14 15:51:11,206 Loading section: Shed Installs -galaxy.tools.toolbox.base DEBUG 2016-04-14 15:51:11,387 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3, version: 2.1.3 into tool panel.... -galaxy.tools.deps DEBUG 2016-04-14 15:51:11,389 Unable to find config file './dependency_resolvers_conf.xml' -galaxy.tools.search DEBUG 2016-04-14 15:51:11,458 Starting to build toolbox index. -galaxy.tools.search DEBUG 2016-04-14 15:51:11,851 Toolbox index finished. -galaxy.tools.data_manager.manager DEBUG 2016-04-14 15:51:11,854 Loaded Data Manager: test_data_manager -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,857 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,859 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. -galaxy.datatypes.display_applications.application ERROR 2016-04-14 15:51:11,862 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,862 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,863 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,863 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,864 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,866 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,867 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,869 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,870 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,876 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. -galaxy.datatypes.display_applications.application ERROR 2016-04-14 15:51:11,878 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,878 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,879 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,885 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,894 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,895 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. -galaxy.datatypes.display_applications.application ERROR 2016-04-14 15:51:11,897 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,897 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,900 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,903 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. -galaxy.datatypes.display_applications.application ERROR 2016-04-14 15:51:11,905 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,905 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,906 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,907 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. -galaxy.datatypes.display_applications.application ERROR 2016-04-14 15:51:11,909 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,909 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,910 Adding inherited display application 'ensembl_gff' to datatype 'gtf' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,910 Adding inherited display application 'igv_gff' to datatype 'gtf' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,910 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,910 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,911 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,911 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,911 Adding inherited display application 'ensembl_interval' to datatype 'bed12' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,911 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,911 Adding inherited display application 'rviewer_interval' to datatype 'bed12' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,911 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'ensembl_interval' to datatype 'chrint' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'rviewer_interval' to datatype 'chrint' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'ensembl_interval' to datatype 'bed' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'rviewer_interval' to datatype 'bed' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,914 Adding inherited display application 'ensembl_gff' to datatype 'gff3' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,914 Adding inherited display application 'igv_gff' to datatype 'gff3' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,914 Adding inherited display application 'ensembl_interval' to datatype 'bed6' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,914 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,914 Adding inherited display application 'rviewer_interval' to datatype 'bed6' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,914 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,916 Loaded converter: CONVERTER_Bam_Bai_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,917 Loaded converter: CONVERTER_bam_to_bigwig_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,918 Loaded converter: CONVERTER_bed_to_gff_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,919 Loaded converter: CONVERTER_bed_to_bgzip_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,920 Loaded converter: CONVERTER_bed_to_tabix_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,921 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,922 Loaded converter: CONVERTER_bed_to_fli_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,923 Loaded converter: CONVERTER_bedgraph_to_bigwig -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,924 Loaded converter: CONVERTER_len_to_linecount -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,925 Loaded converter: CONVERTER_interval_to_bgzip_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,926 Loaded converter: CONVERTER_interval_to_tabix_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,928 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,928 Loaded converter: CONVERTER_fasta_to_tabular -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,930 Loaded converter: CONVERTER_fasta_to_bowtie_base_index -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,931 Loaded converter: CONVERTER_fasta_to_bowtie_color_index -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,932 Loaded converter: CONVERTER_fasta_to_2bit -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,933 Loaded converter: CONVERTER_fasta_to_len -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,934 Loaded converter: CONVERTER_fastq_to_fqtoc0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,935 Loaded converter: CONVERTER_fastq_to_fqtoc0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,936 Loaded converter: CONVERTER_fastq_to_fqtoc0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,937 Loaded converter: CONVERTER_fastq_to_fqtoc0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,938 Loaded converter: CONVERTER_fastq_to_fqtoc0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,939 Loaded converter: CONVERTER_gff_to_bed_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,940 Loaded converter: CONVERTER_gff_to_interval_index_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,941 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,942 Loaded converter: CONVERTER_gff_to_fli_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,943 Loaded converter: CONVERTER_gff_to_interval_index_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,944 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,945 Loaded converter: CONVERTER_interval_to_bed_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,946 Loaded converter: CONVERTER_interval_to_bedstrict_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,947 Loaded converter: CONVERTER_interval_to_bed6_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,948 Loaded converter: CONVERTER_interval_to_bed12_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,949 Loaded converter: CONVERTER_interval_to_bgzip_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,950 Loaded converter: CONVERTER_interval_to_tabix_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,951 Loaded converter: CONVERTER_interval_to_bigwig_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,952 Loaded converter: CONVERTER_picard_interval_list_to_bed6 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,953 Loaded converter: CONVERTER_maf_to_fasta_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,954 Loaded converter: CONVERTER_maf_to_interval_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,957 Loaded converter: CONVERTER_encodepeak_to_tabix_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,957 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,959 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,960 Loaded converter: CONVERTER_interval_to_bgzip_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,961 Loaded converter: CONVERTER_interval_to_tabix_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,962 Loaded converter: CONVERTER_sam_to_bam -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,963 Loaded converter: CONVERTER_sam_to_bigwig_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,964 Loaded converter: tabular_to_dbnsfp -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,965 Loaded converter: CONVERTER_vcf_to_bgzip_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,966 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,967 Loaded converter: CONVERTER_vcf_to_tabix_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,968 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,969 Loaded converter: CONVERTER_wig_to_bigwig -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,970 Loaded converter: CONVERTER_wiggle_to_interval_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,971 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,972 Loaded converter: lped2fpedconvert -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,973 Loaded converter: lped2pbedconvert -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,974 Loaded converter: pbed2lpedconvert -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,975 Loaded converter: pbed2ldindepconvert -galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,977 Loaded external metadata tool: __SET_METADATA__ -galaxy.tools.special_tools DEBUG 2016-04-14 15:51:11,978 Loaded history import tool: __IMPORT_HISTORY__ -galaxy.tools.special_tools DEBUG 2016-04-14 15:51:11,980 Loaded history export tool: __EXPORT_HISTORY__ -galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,981 VisualizationsRegistry, loaded plugin: charts -galaxy.visualization.plugins.config_parser INFO 2016-04-14 15:51:11,982 Visualizations plugin disabled: Circster. Skipping... -galaxy.visualization.plugins.config_parser INFO 2016-04-14 15:51:11,982 template syntax is deprecated: use entry_point instead -galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,983 VisualizationsRegistry, loaded plugin: csg -galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,983 VisualizationsRegistry, loaded plugin: graphview -galaxy.visualization.plugins.config_parser INFO 2016-04-14 15:51:11,984 template syntax is deprecated: use entry_point instead -galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,984 VisualizationsRegistry, loaded plugin: graphviz -galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,985 VisualizationsRegistry, loaded plugin: phyloviz -galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,986 VisualizationsRegistry, loaded plugin: scatterplot -galaxy.visualization.plugins.config_parser INFO 2016-04-14 15:51:11,987 Visualizations plugin disabled: Sweepster. Skipping... -galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,988 VisualizationsRegistry, loaded plugin: trackster -galaxy.tours INFO 2016-04-14 15:51:12,032 Loaded tour 'core.galaxy_ui' -galaxy.tours INFO 2016-04-14 15:51:12,065 Loaded tour 'core.history' -galaxy.jobs.manager DEBUG 2016-04-14 15:51:12,069 Starting job handler -galaxy.jobs INFO 2016-04-14 15:51:12,069 Handler 'main' will load all configured runner plugins -galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-14 15:51:12,069 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit -galaxy.jobs.runners DEBUG 2016-04-14 15:51:12,069 Starting 5 LocalRunner workers -galaxy.jobs DEBUG 2016-04-14 15:51:12,071 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' -galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-14 15:51:12,072 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit -galaxy.jobs.runners DEBUG 2016-04-14 15:51:12,073 Starting 2 TaskRunner workers -galaxy.jobs DEBUG 2016-04-14 15:51:12,073 Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks' -galaxy.jobs DEBUG 2016-04-14 15:51:12,073 Legacy destination with id 'local:///', url 'local:///' converted, got params: -galaxy.jobs.handler DEBUG 2016-04-14 15:51:12,073 Loaded job runners plugins: tasks:local -galaxy.jobs.handler INFO 2016-04-14 15:51:12,074 job handler stop queue started -galaxy.jobs.handler INFO 2016-04-14 15:51:12,091 job handler queue started -galaxy.sample_tracking.external_service_types DEBUG 2016-04-14 15:51:12,098 Loaded external_service_type: Simple unknown sequencer 1.0.0 -galaxy.sample_tracking.external_service_types DEBUG 2016-04-14 15:51:12,100 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 -galaxy.workflow.scheduling_manager DEBUG 2016-04-14 15:51:12,103 Starting workflow schedulers -functional_tests.py INFO 2016-04-14 15:51:12,110 Embedded Universe application started -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,117 Enabling 'external_service' controller, class: ExternalService -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,120 Enabling 'dataset' controller, class: DatasetInterface -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,121 Enabling 'requests' controller, class: Requests -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,121 Enabling 'userskeys' controller, class: User -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,123 Enabling 'history' controller, class: HistoryController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,126 Enabling 'root' controller, class: RootController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,126 Enabling 'tool_runner' controller, class: ToolRunner -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,128 Enabling 'user' controller, class: User -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,134 Enabling 'visualization' controller, class: VisualizationController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,134 Enabling 'requests_common' controller, class: RequestsCommon -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,134 Enabling 'error' controller, class: Error -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,135 Enabling 'request_type' controller, class: RequestType -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,135 Enabling 'biostar' controller, class: BiostarController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,135 Enabling 'search' controller, class: SearchController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,136 Enabling 'data_manager' controller, class: DataManager -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,136 Enabling 'mobile' controller, class: Mobile -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,203 Enabling 'admin_toolshed' controller, class: AdminGalaxy -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,203 Enabling 'admin_toolshed' controller, class: AdminToolshed -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,204 Enabling 'external_services' controller, class: ExternalServiceController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,204 Enabling 'library_admin' controller, class: LibraryAdmin -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,205 Enabling 'forms' controller, class: Forms -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,205 Enabling 'tag' controller, class: TagsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,207 Enabling 'workflow' controller, class: WorkflowController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,208 Enabling 'page' controller, class: PageController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,208 Enabling 'async' controller, class: ASync -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,209 Enabling 'requests_admin' controller, class: RequestsAdmin -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,209 Enabling 'library' controller, class: Library -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,209 Enabling 'library_common' controller, class: LibraryCommon -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,209 Enabling 'admin' controller, class: AdminGalaxy -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,211 Enabling 'requests' API controller, class: RequestsAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,212 Enabling 'libraries' API controller, class: LibrariesController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,213 Enabling 'histories' API controller, class: HistoriesController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,213 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,214 Enabling 'configuration' API controller, class: ConfigurationController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,214 Enabling 'tours' API controller, class: ToursController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,215 Enabling 'remote_files' API controller, class: RemoteFilesAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,215 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,215 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,216 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,216 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,216 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,216 Enabling 'group_roles' API controller, class: GroupRolesAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,217 Enabling 'quotas' API controller, class: QuotaAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,217 Enabling 'folders' API controller, class: FoldersController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,218 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,218 Enabling 'page_revisions' API controller, class: PageRevisionsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,218 Enabling 'pages' API controller, class: PagesController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,218 Enabling 'roles' API controller, class: RoleAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,219 Enabling 'genomes' API controller, class: GenomesController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,219 Enabling 'metrics' API controller, class: MetricsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,219 Enabling 'library_contents' API controller, class: LibraryContentsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,220 Enabling 'visualizations' API controller, class: VisualizationsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,220 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,220 Enabling 'history_tags' API controller, class: HistoryTagsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,220 Enabling 'workflow_tags' API controller, class: WorkflowTagsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,221 Enabling 'jobs' API controller, class: JobController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,238 Enabling 'search' API controller, class: SearchController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,238 Enabling 'workflows' API controller, class: WorkflowsAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,239 Enabling 'tools' API controller, class: ToolsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,240 Enabling 'request_types' API controller, class: RequestTypeAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,240 Enabling 'datasets' API controller, class: DatasetsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,240 Enabling 'group_users' API controller, class: GroupUsersAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,241 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,241 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,242 Enabling 'history_contents' API controller, class: HistoryContentsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,242 Enabling 'forms' API controller, class: FormDefinitionAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,242 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,243 Enabling 'datatypes' API controller, class: DatatypesController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,243 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,244 Enabling 'samples' API controller, class: SamplesAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,244 Enabling 'folder_contents' API controller, class: FolderContentsController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,244 Enabling 'job_files' API controller, class: JobFilesAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,245 Enabling 'users' API controller, class: UserAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,245 Enabling 'groups' API controller, class: GroupAPIController -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,245 Enabling 'tool_data' API controller, class: ToolData -galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,246 Enabling 'authenticate' API controller, class: AuthenticationController -galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,706 Enabling 'httpexceptions' middleware -galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,707 Enabling 'recursive' middleware -galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,716 Enabling 'error' middleware -galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,716 Enabling 'x-forwarded-host' middleware -galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,716 Enabling 'Request ID' middleware -galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,722 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static -galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,722 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static -galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,722 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static -galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,722 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static -galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,722 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static -galaxy.queue_worker INFO 2016-04-14 15:51:12,723 Binding and starting galaxy control worker for main -functional_tests.py DEBUG 2016-04-14 15:51:12,732 Attempting to serve app on randomly chosen port: 9732 -functional_tests.py INFO 2016-04-14 15:51:12,874 Embedded web server started -functional_tests.py INFO 2016-04-14 15:51:12,875 Functional tests will be run against localhost:9732 -galaxy.tools.toolbox.watcher INFO 2016-04-14 15:51:12,876 Watchdog library unavailble, cannot monitor tools. -galaxy.tools.toolbox.base INFO 2016-04-14 15:51:12,876 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/tool_conf.xml -galaxy.tools.toolbox.base INFO 2016-04-14 15:51:12,876 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/config/shed_tool_conf.xml -galaxy.tools.toolbox.base INFO 2016-04-14 15:51:12,902 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/empty_tool_conf.xml -galaxy.tools.toolbox.base INFO 2016-04-14 15:51:12,902 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/config/shed_tool_conf.xml -galaxy.tools.toolbox.base DEBUG 2016-04-14 15:51:12,980 Loaded tool id: upload1, version: 1.1.4 into tool panel.. -galaxy.tools.toolbox.base DEBUG 2016-04-14 15:51:12,980 Loading section: Shed Installs -galaxy.tools.toolbox.base DEBUG 2016-04-14 15:51:13,221 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3, version: 2.1.3 into tool panel.... -galaxy.tools.deps DEBUG 2016-04-14 15:51:13,221 Unable to find config file './dependency_resolvers_conf.xml' -[?1034hbase.asserts DEBUG 2016-04-14 15:51:13,594 base.asserts.text -base.asserts DEBUG 2016-04-14 15:51:13,595 base.asserts.tabular -base.asserts DEBUG 2016-04-14 15:51:13,595 base.asserts.xml -nose.plugins.manager DEBUG 2016-04-14 15:51:13,605 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:13,786 Starting new HTTP connection (1): localhost -galaxy.web.framework.webapp INFO 2016-04-14 15:51:13,791 Session authenticated using Galaxy master api key -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:13,802 "GET /api/users?key=test_key HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:14,070 Starting new HTTP connection (1): localhost -galaxy.web.framework.webapp INFO 2016-04-14 15:51:14,073 Session authenticated using Galaxy master api key -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:14,563 "POST /api/users HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:14,564 Starting new HTTP connection (1): localhost -galaxy.web.framework.webapp INFO 2016-04-14 15:51:14,570 Session authenticated using Galaxy master api key -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:14,637 "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:14,639 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:14,809 "POST /api/histories HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:14,825 Starting new HTTP connection (1): localhost -galaxy.tools DEBUG 2016-04-14 15:51:15,045 Validated and populated state for tool request (19.760 ms) -galaxy.tools.actions.upload DEBUG 2016-04-14 15:51:15,091 Persisted uploads (22.581 ms) -galaxy.tools.actions.upload DEBUG 2016-04-14 15:51:15,578 Checked and cleaned uploads (487.187 ms) -galaxy.tools.actions.upload_common INFO 2016-04-14 15:51:15,694 tool upload1 created job id 1 -galaxy.tools.actions.upload DEBUG 2016-04-14 15:51:15,821 Created upload job (242.417 ms) -galaxy.tools.execute DEBUG 2016-04-14 15:51:15,821 Tool [upload1] created job [1] (752.711 ms) -galaxy.tools.execute DEBUG 2016-04-14 15:51:15,840 Executed all jobs for tool request: (795.117 ms) -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:15,876 "POST /api/tools HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:15,878 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:15,962 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:15,964 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,048 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,050 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,134 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,136 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,220 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,222 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,302 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,304 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,392 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,394 Starting new HTTP connection (1): localhost -galaxy.jobs DEBUG 2016-04-14 15:51:16,469 (1) Working directory for job is: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1 -galaxy.jobs.handler DEBUG 2016-04-14 15:51:16,519 (1) Dispatching to local runner -galaxy.jobs DEBUG 2016-04-14 15:51:16,623 (1) Persisting job destination (destination id: local:///) -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,655 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,657 Starting new HTTP connection (1): localhost -galaxy.jobs.runners DEBUG 2016-04-14 15:51:16,713 Job [1] queued (194.097 ms) -galaxy.jobs.handler INFO 2016-04-14 15:51:16,754 (1) Job dispatched -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,930 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,933 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:17,176 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:17,177 Starting new HTTP connection (1): localhost -galaxy.tools.deps DEBUG 2016-04-14 15:51:17,460 Building dependency shell command for dependency 'samtools' -galaxy.tools.deps DEBUG 2016-04-14 15:51:17,460 Find dependency samtools version None -galaxy.tools.deps DEBUG 2016-04-14 15:51:17,461 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps DEBUG 2016-04-14 15:51:17,461 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps DEBUG 2016-04-14 15:51:17,461 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps DEBUG 2016-04-14 15:51:17,462 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps DEBUG 2016-04-14 15:51:17,462 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:17,462 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -galaxy.tools.deps WARNING 2016-04-14 15:51:17,462 Failed to resolve dependency on 'samtools', ignoring -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:17,467 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:17,579 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -galaxy.jobs.command_factory INFO 2016-04-14 15:51:17,580 Built script [/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/tools/data_source/upload.py /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev /tmp/714401.1.short.q/tmpAQxCGj/tmp/tmpLPOdzn /tmp/714401.1.short.q/tmpAQxCGj/tmp/tmp0jkGJc 1:/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/dataset_1_files:/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat] -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:17,585 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:17,877 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:17,879 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:18,065 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:18,067 Starting new HTTP connection (1): localhost -galaxy.jobs.runners DEBUG 2016-04-14 15:51:18,069 (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 2016-04-14 15:51:18,085 (1) executing job script: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/galaxy_1.sh -galaxy.jobs DEBUG 2016-04-14 15:51:18,094 (1) Persisting job destination (destination id: local:///) -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:18,245 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -galaxy.jobs.runners.local DEBUG 2016-04-14 15:51:21,083 execution finished: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/galaxy_1.sh -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:21,084 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:21,293 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:21,295 Starting new HTTP connection (1): localhost -galaxy.datatypes.metadata DEBUG 2016-04-14 15:51:21,348 loading metadata from file for: HistoryDatasetAssociation 1 -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:21,606 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:21,608 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:21,789 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:21,791 Starting new HTTP connection (1): localhost -galaxy.tools DEBUG 2016-04-14 15:51:21,898 Validated and populated state for tool request (72.417 ms) -galaxy.tools.actions INFO 2016-04-14 15:51:22,068 Handled output (99.542 ms) -galaxy.jobs DEBUG 2016-04-14 15:51:22,129 job 1 ended (finish() executed in (1044.369 ms)) -galaxy.tools.actions INFO 2016-04-14 15:51:22,213 Handled output (144.572 ms) -galaxy.tools.actions INFO 2016-04-14 15:51:22,303 Handled output (90.577 ms) -galaxy.tools.actions INFO 2016-04-14 15:51:22,388 Handled output (84.692 ms) -galaxy.tools.actions INFO 2016-04-14 15:51:22,477 Verified access to datasets (7.993 ms) -galaxy.tools.execute DEBUG 2016-04-14 15:51:22,596 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 2016-04-14 15:51:22,614 Executed all jobs for tool request: (715.204 ms) -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:22,719 "POST /api/tools HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:22,721 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:22,870 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -galaxy.jobs DEBUG 2016-04-14 15:51:23,004 (2) Working directory for job is: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2 -galaxy.jobs.handler DEBUG 2016-04-14 15:51:23,020 (2) Dispatching to local runner -galaxy.jobs DEBUG 2016-04-14 15:51:23,062 (2) Persisting job destination (destination id: local:///) -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:23,073 Starting new HTTP connection (1): localhost -galaxy.jobs.runners DEBUG 2016-04-14 15:51:23,141 Job [2] queued (121.409 ms) -galaxy.jobs.handler INFO 2016-04-14 15:51:23,213 (2) Job dispatched -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:23,326 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,695 Building dependency shell command for dependency 'R' -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,696 Find dependency R version 3.1.2 -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,704 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b7e7c239b10> (isnull? False) -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,704 Building dependency shell command for dependency 'r-snow' -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,704 Find dependency r-snow version 0.4_1 -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,704 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps WARNING 2016-04-14 15:51:23,705 Failed to resolve dependency on 'r-snow', ignoring -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Building dependency shell command for dependency 'bioconductor-camera' -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Find dependency bioconductor-camera version 1.22.0 -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b7e7c268890> (isnull? False) -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Building dependency shell command for dependency 'r-batch' -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Find dependency r-batch version 1.1_4 -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) -galaxy.tools.deps WARNING 2016-04-14 15:51:23,706 Failed to resolve dependency on 'r-batch', ignoring -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Building dependency shell command for dependency 'graphicsmagick' -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Find dependency graphicsmagick version 1.3.20 -galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b7ec80fead0> (isnull? False) -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:23,729 Starting new HTTP connection (1): localhost -galaxy.jobs.command_factory INFO 2016-04-14 15:51:23,830 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 ${GALAXY_SLOTS:-1} sigma 6 perfwhm 0.6 maxcharge 3 maxiso 4 minfrac 0.5 ppm 5 mzabs 0.015 intval into max_peaks 100 quick FALSE polarity negative cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE multiplier 3 runDiffreport TRUE eicmax 200 eicwidth 200 value into sortpval FALSE h 480 w 640 mzdec 2 new_file_path /tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_] -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:23,968 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:24,771 Starting new HTTP connection (1): localhost -galaxy.jobs.runners DEBUG 2016-04-14 15:51:24,772 (2) command is: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/tool_script.sh; return_code=$?; 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 2016-04-14 15:51:24,795 (2) executing job script: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/galaxy_2.sh -galaxy.jobs DEBUG 2016-04-14 15:51:24,808 (2) Persisting job destination (destination id: local:///) -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:25,115 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -galaxy.jobs.runners.local DEBUG 2016-04-14 15:51:47,359 execution finished: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/galaxy_2.sh -galaxy.jobs.output_checker INFO 2016-04-14 15:51:47,404 Job 2: Fatal error: Exit code 1 () -galaxy.jobs.output_checker DEBUG 2016-04-14 15:51:47,404 Tool exit code indicates an error, failing job. -galaxy.jobs DEBUG 2016-04-14 15:51:47,491 (2) setting dataset 2 state to ERROR -galaxy.jobs DEBUG 2016-04-14 15:51:47,531 (2) setting dataset 3 state to ERROR -galaxy.jobs DEBUG 2016-04-14 15:51:47,571 (2) setting dataset 4 state to ERROR -galaxy.jobs DEBUG 2016-04-14 15:51:47,610 (2) setting dataset 5 state to ERROR -galaxy.jobs DEBUG 2016-04-14 15:51:48,011 job 2 ended (finish() executed in (650.423 ms)) -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:48,962 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,130 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,136 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,196 "GET /api/histories/2891970512fa2d5a/contents?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,198 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,375 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,377 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,509 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,511 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,680 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,682 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,805 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,808 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,997 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,999 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:50,149 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:50,152 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:50,490 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:50,492 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:50,615 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:50,617 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:50,786 "GET /api/jobs/5729865256bc2525?full=true&key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:50,788 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:50,969 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:50,971 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,027 "GET /api/histories/2891970512fa2d5a/contents?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,028 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,229 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,231 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,352 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,354 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,547 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,549 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,669 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,672 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,842 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,844 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,963 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,965 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:52,209 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:52,212 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:52,336 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:52,339 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:52,493 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:52,496 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:52,565 "GET /api/histories/2891970512fa2d5a/contents?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:52,567 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:52,739 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:52,741 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:52,859 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:52,862 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:53,031 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:53,033 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:53,191 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:53,193 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:53,361 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:53,363 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:53,479 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:53,482 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:53,669 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:53,671 Starting new HTTP connection (1): localhost -requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:53,793 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None -functional_tests.py INFO 2016-04-14 15:51:53,821 Shutting down -functional_tests.py INFO 2016-04-14 15:51:53,821 Shutting down embedded web server -functional_tests.py INFO 2016-04-14 15:51:53,823 Embedded web server stopped -functional_tests.py INFO 2016-04-14 15:51:53,823 Shutting down app -galaxy.jobs.handler INFO 2016-04-14 15:51:53,824 sending stop signal to worker thread -galaxy.jobs.handler INFO 2016-04-14 15:51:53,824 job handler queue stopped -galaxy.jobs.runners INFO 2016-04-14 15:51:53,824 TaskRunner: Sending stop signal to 2 worker threads -galaxy.jobs.runners INFO 2016-04-14 15:51:53,824 LocalRunner: Sending stop signal to 5 worker threads -galaxy.jobs.handler INFO 2016-04-14 15:51:53,825 sending stop signal to worker thread -galaxy.jobs.handler INFO 2016-04-14 15:51:53,825 job handler stop queue stopped -functional_tests.py INFO 2016-04-14 15:51:53,826 Embedded Universe application stopped -functional_tests.py INFO 2016-04-14 15:51:53,826 Cleaning up temporary files in /tmp/714401.1.short.q/tmpYE8cIL/tmpVeogQe -galaxy.jobs.handler INFO 2016-04-14 15:51:54,673 sending stop signal to worker thread -galaxy.jobs.handler INFO 2016-04-14 15:51:54,673 job handler queue stopped -galaxy.jobs.runners INFO 2016-04-14 15:51:54,673 TaskRunner: Sending stop signal to 2 worker threads -galaxy.jobs.runners INFO 2016-04-14 15:51:54,673 LocalRunner: Sending stop signal to 5 worker threads -galaxy.jobs.handler INFO 2016-04-14 15:51:54,674 sending stop signal to worker thread -galaxy.jobs.handler INFO 2016-04-14 15:51:54,674 job handler stop queue stopped +[('app:main', 'new_file_path', '/tmp/714419.1.short.q/tmp6xBwof/tmpacHkJy/new_files_path_3hEYGU'), ('app:main', 'database_connection', 'sqlite:////tmp/714419.1.short.q/tmp6xBwof/tmpacHkJy/database/universe.sqlite'), ('app:main', 'data_manager_config_file', 'config/data_manager_conf.xml.sample,test/functional/tools/sample_data_manager_conf.xml'), ('app:main', 'job_queue_workers', 5), ('app:main', 'log_destination', 'stdout'), ('app:main', 'allow_user_deletion', True), ('app:main', 'master_api_key', 'test_key'), ('app:main', 'tool_config_file', '/tmp/714419.1.short.q/tmpUKxFhz'), ('app:main', 'template_cache_path', '/tmp/714419.1.short.q/tmp6xBwof/tmpacHkJy/database/compiled_templates'), ('app:main', 'job_working_directory', '/tmp/714419.1.short.q/tmp6xBwof/tmpacHkJy/job_working_directory_faEKBn'), ('app:main', 'tool_dependency_dir', '/tmp/714419.1.short.q/tmp6zzhM3/deps'), ('app:main', 'check_migrate_tools', False), ('app:main', 'tool_path', 'tools'), ('app:main', 'enable_beta_tool_formats', True), ('app:main', 'user_library_import_dir', None), ('app:main', 'galaxy_data_manager_data_path', '/tmp/714419.1.short.q/tmp6xBwof/data_manager_test_tmp8bCYlG/data_manager_tool-data1dSWwR'), ('app:main', 'tool_data_table_config_path', 'config/tool_data_table_conf.xml.sample,test/functional/tool-data/sample_tool_data_tables.xml'), ('app:main', 'file_path', '/tmp/714419.1.short.q/tmp6xBwof/tmpacHkJy/database/files'), ('app:main', 'datatype_converters_config_file', 'datatype_converters_conf.xml.sample'), ('app:main', 'database_auto_migrate', True), ('app:main', 'use_tasked_jobs', True), ('app:main', 'auto_configure_logging', True), ('app:main', 'tool_parse_help', False), ('app:main', 'shed_tool_data_table_config', 'config/shed_tool_data_table_conf.xml'), ('app:main', 'update_integrated_tool_panel', False), ('app:main', 'admin_users', 'test@bx.psu.edu'), ('app:main', 'template_path', 'templates'), ('app:main', 'allow_user_creation', True), ('app:main', 'use_heartbeat', False), ('app:main', 'allow_library_path_paste', True), ('app:main', 'api_allow_run_as', 'test@bx.psu.edu'), ('app:main', 'test_conf', 'test.conf'), ('app:main', 'id_secret', 'changethisinproductiontoo'), ('app:main', 'library_import_dir', None), ('app:main', 'cleanup_job', 'onsuccess'), ('app:main', 'running_functional_tests', True)] +galaxy.queue_worker INFO 2016-04-14 16:47:16,672 Initalizing main Galaxy Queue Worker on sqlalchemy+sqlite:// +tool_shed.tool_shed_registry DEBUG 2016-04-14 16:47:16,721 Loading references to tool sheds from /tmp/714419.1.short.q/tmp6zzhM3/tool_sheds_conf.xml +tool_shed.tool_shed_registry DEBUG 2016-04-14 16:47:16,722 Loaded reference to tool shed: Target Shed +galaxy.app DEBUG 2016-04-14 16:47:16,723 Using "galaxy.ini" config file: /tmp/714419.1.short.q/tmp6xBwof/functional_tests_wsgi.ini +migrate.versioning.repository DEBUG 2016-04-14 16:47:16,813 Loading repository lib/galaxy/model/migrate... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Loading script 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+migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Loading script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Loading script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Loading script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 Loading script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 Script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 Loading script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 Script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 Loading script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 Script 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+migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,835 Loading script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,835 Script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,835 Loading script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,835 Script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,835 Loading script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,835 Script 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2016-04-14 16:47:16,836 Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,836 Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... +migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully +migrate.versioning.repository DEBUG 2016-04-14 16:47:16,838 Repository lib/galaxy/model/migrate loaded successfully +migrate.versioning.repository DEBUG 2016-04-14 16:47:16,839 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) +galaxy.config INFO 2016-04-14 16:47:16,909 Install database targetting Galaxy's database configuration. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,961 Loading datatypes from /tmp/714419.1.short.q/tmp6zzhM3/tmp/tmp-toolshed-acalpd4oJfOX +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,966 Loading datatypes from /tmp/714419.1.short.q/tmp6zzhM3/tmp/tmp-toolshed-acalpdGiP3GN +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,966 Exception importing proprietary code file /tmp/714419.1.short.q/tmp6zzhM3/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/rdata_xcms_datatypes/bff835d58914/rdata_xcms_datatypes/binary: No module named binary +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,966 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,984 Loading datatypes from ./config/datatypes_conf.xml.sample +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,985 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,985 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,986 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,987 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,987 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,987 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,987 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,987 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,988 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,988 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,988 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,988 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,988 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,988 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,989 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,989 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,989 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,989 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,990 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,990 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,990 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,990 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,991 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,991 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,991 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,991 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,991 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,992 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,992 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,992 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,992 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,992 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,992 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,993 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,993 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,993 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,993 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,993 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,993 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,994 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,994 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,994 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,994 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,994 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,994 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,995 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,995 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,995 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,995 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,996 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,996 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,996 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,996 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,997 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,997 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,997 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,997 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,997 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,997 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,998 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,998 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,998 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,998 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,998 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,998 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,999 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,999 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,001 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,001 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,001 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,002 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,002 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,002 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,002 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,003 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,003 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,003 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,003 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,003 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,003 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,004 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,004 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,004 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,004 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,004 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,004 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,005 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,005 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,005 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,005 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,005 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,005 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,006 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,006 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,006 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,006 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,006 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,006 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,007 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,007 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,007 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,007 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,007 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,007 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,008 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,008 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,008 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,008 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,008 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,008 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,009 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,009 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,009 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,009 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,009 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,009 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,010 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,010 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,010 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,010 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,010 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,010 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,011 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,011 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,011 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,011 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,011 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,011 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,012 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,012 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,012 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,012 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,012 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,012 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,013 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,013 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,013 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,013 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,013 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,013 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,014 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,014 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,014 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,014 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,014 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,015 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,015 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,015 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,015 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,019 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,019 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,019 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,020 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,020 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,020 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,020 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,020 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,021 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,021 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,021 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,021 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,021 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,021 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,022 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,022 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,022 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,022 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,022 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,022 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,023 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,024 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,024 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,025 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,025 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,025 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,025 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,025 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,026 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,028 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,028 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,028 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,028 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,028 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,029 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,029 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,029 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,029 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,031 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,031 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,031 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,031 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,032 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,032 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,032 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,032 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,033 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,033 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,033 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,033 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,033 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,034 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,034 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,034 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,034 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,039 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,039 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,039 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,039 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,040 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,040 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,040 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,040 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,042 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,042 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,042 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,042 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,042 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,043 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,043 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,043 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,043 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,044 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,044 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,044 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,044 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,044 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,045 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,045 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,045 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,045 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,046 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,046 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,046 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,046 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,047 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,047 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,048 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,048 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,048 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,048 Overriding conflicting datatype with extension 'rdata', using datatype from ./config/datatypes_conf.xml.sample. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,048 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,048 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,049 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,049 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,049 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,049 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,050 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,050 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,051 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,051 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,051 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,051 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Removed conflicting sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Removed conflicting sniffer for datatype 'galaxy.datatypes.images:Html' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,064 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,064 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,064 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,064 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,064 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,064 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,066 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,066 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,066 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,066 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,066 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,066 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,067 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,067 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt +galaxy.jobs WARNING 2016-04-14 16:47:17,140 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/714419.1.short.q/tmp6xBwof/functional_tests_wsgi.ini" instead +galaxy.jobs DEBUG 2016-04-14 16:47:17,140 Loading job configuration from /tmp/714419.1.short.q/tmp6xBwof/functional_tests_wsgi.ini +galaxy.jobs DEBUG 2016-04-14 16:47:17,140 Done loading job configuration +beaker.container DEBUG 2016-04-14 16:47:17,171 data file /tmp/714419.1.short.q/tmp6zzhM3/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache +galaxy.tools.toolbox.watcher INFO 2016-04-14 16:47:17,172 Watchdog library unavailble, cannot monitor tools. +galaxy.tools.toolbox.base INFO 2016-04-14 16:47:17,172 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-14 16:47:17,186 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/config/shed_tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-14 16:47:17,233 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/empty_tool_conf.xml +galaxy.tools.toolbox.base DEBUG 2016-04-14 16:47:17,233 Loaded tool id: upload1, version: 1.1.4 into tool panel.. +galaxy.tools.toolbox.base DEBUG 2016-04-14 16:47:17,233 Loading section: Shed Installs +galaxy.tools.toolbox.base DEBUG 2016-04-14 16:47:17,463 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3, version: 2.1.3 into tool panel.... +galaxy.tools.deps DEBUG 2016-04-14 16:47:17,465 Unable to find config file './dependency_resolvers_conf.xml' +galaxy.tools.search DEBUG 2016-04-14 16:47:17,552 Starting to build toolbox index. +galaxy.tools.search DEBUG 2016-04-14 16:47:18,060 Toolbox index finished. +galaxy.tools.data_manager.manager DEBUG 2016-04-14 16:47:18,064 Loaded Data Manager: test_data_manager +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,068 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,072 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-04-14 16:47:18,075 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,075 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,076 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,077 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,077 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,081 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,081 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,085 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,085 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,094 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.display_applications.application ERROR 2016-04-14 16:47:18,096 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,097 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,097 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,106 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,118 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,119 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. +galaxy.datatypes.display_applications.application ERROR 2016-04-14 16:47:18,123 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,123 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,126 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,130 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-04-14 16:47:18,133 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,133 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,134 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,135 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. +galaxy.datatypes.display_applications.application ERROR 2016-04-14 16:47:18,139 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,139 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,139 Adding inherited display application 'ensembl_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,139 Adding inherited display application 'igv_gff' to datatype 'gtf' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,140 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,140 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,140 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,141 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,141 Adding inherited display application 'ensembl_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,141 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,141 Adding inherited display application 'rviewer_interval' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,141 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,142 Adding inherited display application 'ensembl_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,142 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,142 Adding inherited display application 'rviewer_interval' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,142 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,143 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,143 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,143 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,143 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'ensembl_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'rviewer_interval' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,145 Adding inherited display application 'ensembl_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,145 Adding inherited display application 'igv_gff' to datatype 'gff3' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,145 Adding inherited display application 'ensembl_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,146 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,146 Adding inherited display application 'rviewer_interval' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,146 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,148 Loaded converter: CONVERTER_Bam_Bai_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,149 Loaded converter: CONVERTER_bam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,151 Loaded converter: CONVERTER_bed_to_gff_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,152 Loaded converter: CONVERTER_bed_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,154 Loaded converter: CONVERTER_bed_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,155 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,156 Loaded converter: CONVERTER_bed_to_fli_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,158 Loaded converter: CONVERTER_bedgraph_to_bigwig +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,159 Loaded converter: CONVERTER_len_to_linecount +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,160 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,162 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,163 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,165 Loaded converter: CONVERTER_fasta_to_tabular +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,166 Loaded converter: CONVERTER_fasta_to_bowtie_base_index +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,168 Loaded converter: CONVERTER_fasta_to_bowtie_color_index +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,169 Loaded converter: CONVERTER_fasta_to_2bit +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,171 Loaded converter: CONVERTER_fasta_to_len +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,172 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,173 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,175 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,176 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,177 Loaded converter: CONVERTER_fastq_to_fqtoc0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,179 Loaded converter: CONVERTER_gff_to_bed_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,180 Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,181 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,182 Loaded converter: CONVERTER_gff_to_fli_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,183 Loaded converter: CONVERTER_gff_to_interval_index_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,184 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,185 Loaded converter: CONVERTER_interval_to_bed_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,186 Loaded converter: CONVERTER_interval_to_bedstrict_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,187 Loaded converter: CONVERTER_interval_to_bed6_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,188 Loaded converter: CONVERTER_interval_to_bed12_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,189 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,190 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,191 Loaded converter: CONVERTER_interval_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,192 Loaded converter: CONVERTER_picard_interval_list_to_bed6 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,193 Loaded converter: CONVERTER_maf_to_fasta_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,194 Loaded converter: CONVERTER_maf_to_interval_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,196 Loaded converter: CONVERTER_encodepeak_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,197 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,198 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,199 Loaded converter: CONVERTER_interval_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,201 Loaded converter: CONVERTER_interval_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,202 Loaded converter: CONVERTER_sam_to_bam +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,203 Loaded converter: CONVERTER_sam_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,204 Loaded converter: tabular_to_dbnsfp +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,205 Loaded converter: CONVERTER_vcf_to_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,206 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,207 Loaded converter: CONVERTER_vcf_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,208 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,209 Loaded converter: CONVERTER_wig_to_bigwig +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,210 Loaded converter: CONVERTER_wiggle_to_interval_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,211 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,212 Loaded converter: lped2fpedconvert +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,213 Loaded converter: lped2pbedconvert +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,214 Loaded converter: pbed2lpedconvert +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,215 Loaded converter: pbed2ldindepconvert +galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,216 Loaded external metadata tool: __SET_METADATA__ +galaxy.tools.special_tools DEBUG 2016-04-14 16:47:18,218 Loaded history import tool: __IMPORT_HISTORY__ +galaxy.tools.special_tools DEBUG 2016-04-14 16:47:18,220 Loaded history export tool: __EXPORT_HISTORY__ +galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,221 VisualizationsRegistry, loaded plugin: charts +galaxy.visualization.plugins.config_parser INFO 2016-04-14 16:47:18,221 Visualizations plugin disabled: Circster. Skipping... +galaxy.visualization.plugins.config_parser INFO 2016-04-14 16:47:18,222 template syntax is deprecated: use entry_point instead +galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,222 VisualizationsRegistry, loaded plugin: csg +galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,223 VisualizationsRegistry, loaded plugin: graphview +galaxy.visualization.plugins.config_parser INFO 2016-04-14 16:47:18,224 template syntax is deprecated: use entry_point instead +galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,224 VisualizationsRegistry, loaded plugin: graphviz +galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,225 VisualizationsRegistry, loaded plugin: phyloviz +galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,226 VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.config_parser INFO 2016-04-14 16:47:18,226 Visualizations plugin disabled: Sweepster. Skipping... +galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,227 VisualizationsRegistry, loaded plugin: trackster +galaxy.tours INFO 2016-04-14 16:47:18,261 Loaded tour 'core.history' +galaxy.tours INFO 2016-04-14 16:47:18,304 Loaded tour 'core.galaxy_ui' +galaxy.jobs.manager DEBUG 2016-04-14 16:47:18,308 Starting job handler +galaxy.jobs INFO 2016-04-14 16:47:18,308 Handler 'main' will load all configured runner plugins +galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-14 16:47:18,308 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners DEBUG 2016-04-14 16:47:18,309 Starting 5 LocalRunner workers +galaxy.jobs DEBUG 2016-04-14 16:47:18,310 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' +galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-14 16:47:18,311 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit +galaxy.jobs.runners DEBUG 2016-04-14 16:47:18,312 Starting 2 TaskRunner workers +galaxy.jobs DEBUG 2016-04-14 16:47:18,312 Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks' +galaxy.jobs DEBUG 2016-04-14 16:47:18,312 Legacy destination with id 'local:///', url 'local:///' converted, got params: +galaxy.jobs.handler DEBUG 2016-04-14 16:47:18,312 Loaded job runners plugins: tasks:local +galaxy.jobs.handler INFO 2016-04-14 16:47:18,313 job handler stop queue started +galaxy.jobs.handler INFO 2016-04-14 16:47:18,332 job handler queue started +galaxy.sample_tracking.external_service_types DEBUG 2016-04-14 16:47:18,340 Loaded external_service_type: Simple unknown sequencer 1.0.0 +galaxy.sample_tracking.external_service_types DEBUG 2016-04-14 16:47:18,343 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 +galaxy.workflow.scheduling_manager DEBUG 2016-04-14 16:47:18,347 Starting workflow schedulers +functional_tests.py INFO 2016-04-14 16:47:18,352 Embedded Universe application started +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,453 Enabling 'admin_toolshed' controller, class: AdminGalaxy +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,453 Enabling 'admin_toolshed' controller, class: AdminToolshed +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,456 Enabling 'history' controller, class: HistoryController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,462 Enabling 'visualization' controller, class: VisualizationController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,464 Enabling 'requests' controller, class: Requests +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,464 Enabling 'async' controller, class: ASync +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,464 Enabling 'admin' controller, class: AdminGalaxy +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,466 Enabling 'mobile' controller, class: Mobile +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,466 Enabling 'external_services' controller, class: ExternalServiceController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,467 Enabling 'tag' controller, class: TagsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,468 Enabling 'biostar' controller, class: BiostarController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,469 Enabling 'root' controller, class: RootController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,469 Enabling 'search' controller, class: SearchController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,470 Enabling 'user' controller, class: User +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,471 Enabling 'data_manager' controller, class: DataManager +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,471 Enabling 'library' controller, class: Library +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,471 Enabling 'error' controller, class: Error +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,471 Enabling 'requests_common' controller, class: RequestsCommon +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,473 Enabling 'page' controller, class: PageController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,474 Enabling 'forms' controller, class: Forms +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,476 Enabling 'workflow' controller, class: WorkflowController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,477 Enabling 'library_admin' controller, class: LibraryAdmin +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,478 Enabling 'external_service' controller, class: ExternalService +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,478 Enabling 'library_common' controller, class: LibraryCommon +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,478 Enabling 'userskeys' controller, class: User +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,479 Enabling 'request_type' controller, class: RequestType +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,480 Enabling 'requests_admin' controller, class: RequestsAdmin +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,480 Enabling 'tool_runner' controller, class: ToolRunner +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,481 Enabling 'dataset' controller, class: DatasetInterface +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,484 Enabling 'group_users' API controller, class: GroupUsersAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,484 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,485 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,485 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,486 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,486 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,486 Enabling 'folders' API controller, class: FoldersController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,487 Enabling 'genomes' API controller, class: GenomesController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,488 Enabling 'history_contents' API controller, class: HistoryContentsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,488 Enabling 'samples' API controller, class: SamplesAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,488 Enabling 'requests' API controller, class: RequestsAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,489 Enabling 'library_contents' API controller, class: LibraryContentsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,490 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,490 Enabling 'users' API controller, class: UserAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,491 Enabling 'pages' API controller, class: PagesController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,492 Enabling 'remote_files' API controller, class: RemoteFilesAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,492 Enabling 'page_revisions' API controller, class: PageRevisionsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,493 Enabling 'folder_contents' API controller, class: FolderContentsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,494 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,494 Enabling 'datasets' API controller, class: DatasetsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,517 Enabling 'search' API controller, class: SearchController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,517 Enabling 'tours' API controller, class: ToursController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,518 Enabling 'request_types' API controller, class: RequestTypeAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,518 Enabling 'groups' API controller, class: GroupAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,519 Enabling 'metrics' API controller, class: MetricsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,519 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,520 Enabling 'histories' API controller, class: HistoriesController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,521 Enabling 'group_roles' API controller, class: GroupRolesAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,522 Enabling 'libraries' API controller, class: LibrariesController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,522 Enabling 'tools' API controller, class: ToolsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,523 Enabling 'roles' API controller, class: RoleAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,523 Enabling 'configuration' API controller, class: ConfigurationController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,524 Enabling 'tool_data' API controller, class: ToolData +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,524 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,524 Enabling 'history_tags' API controller, class: HistoryTagsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,525 Enabling 'workflow_tags' API controller, class: WorkflowTagsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,525 Enabling 'visualizations' API controller, class: VisualizationsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,525 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,526 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,526 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,526 Enabling 'forms' API controller, class: FormDefinitionAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,527 Enabling 'datatypes' API controller, class: DatatypesController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,527 Enabling 'authenticate' API controller, class: AuthenticationController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,527 Enabling 'job_files' API controller, class: JobFilesAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,528 Enabling 'workflows' API controller, class: WorkflowsAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,529 Enabling 'quotas' API controller, class: QuotaAPIController +galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,529 Enabling 'jobs' API controller, class: JobController +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,121 Enabling 'httpexceptions' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,123 Enabling 'recursive' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,133 Enabling 'error' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,133 Enabling 'x-forwarded-host' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,133 Enabling 'Request ID' middleware +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,140 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,140 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,141 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,141 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static +galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,141 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static +galaxy.queue_worker INFO 2016-04-14 16:47:19,141 Binding and starting galaxy control worker for main +functional_tests.py DEBUG 2016-04-14 16:47:19,153 Attempting to serve app on randomly chosen port: 9558 +functional_tests.py INFO 2016-04-14 16:47:19,592 Embedded web server started +functional_tests.py INFO 2016-04-14 16:47:19,592 Functional tests will be run against localhost:9558 +galaxy.tools.toolbox.watcher INFO 2016-04-14 16:47:19,594 Watchdog library unavailble, cannot monitor tools. +galaxy.tools.toolbox.base INFO 2016-04-14 16:47:19,594 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-14 16:47:19,594 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/config/shed_tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-14 16:47:19,626 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/empty_tool_conf.xml +galaxy.tools.toolbox.base INFO 2016-04-14 16:47:19,627 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/config/shed_tool_conf.xml +galaxy.tools.toolbox.base DEBUG 2016-04-14 16:47:19,724 Loaded tool id: upload1, version: 1.1.4 into tool panel.. +galaxy.tools.toolbox.base DEBUG 2016-04-14 16:47:19,724 Loading section: Shed Installs +galaxy.tools.toolbox.base DEBUG 2016-04-14 16:47:19,909 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3, version: 2.1.3 into tool panel.... +galaxy.tools.deps DEBUG 2016-04-14 16:47:19,910 Unable to find config file './dependency_resolvers_conf.xml' +[?1034hbase.asserts DEBUG 2016-04-14 16:47:20,293 base.asserts.text +base.asserts DEBUG 2016-04-14 16:47:20,293 base.asserts.tabular +base.asserts DEBUG 2016-04-14 16:47:20,294 base.asserts.xml +nose.plugins.manager DEBUG 2016-04-14 16:47:20,314 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:20,514 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-04-14 16:47:20,519 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:20,533 "GET /api/users?key=test_key HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:20,788 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-04-14 16:47:20,792 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:21,379 "POST /api/users HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:21,381 Starting new HTTP connection (1): localhost +galaxy.web.framework.webapp INFO 2016-04-14 16:47:21,385 Session authenticated using Galaxy master api key +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:21,446 "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:21,448 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:21,624 "POST /api/histories HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:21,644 Starting new HTTP connection (1): localhost +galaxy.tools DEBUG 2016-04-14 16:47:21,914 Validated and populated state for tool request (26.178 ms) +galaxy.tools.actions.upload DEBUG 2016-04-14 16:47:21,974 Persisted uploads (29.632 ms) +galaxy.tools.actions.upload DEBUG 2016-04-14 16:47:22,425 Checked and cleaned uploads (450.856 ms) +galaxy.tools.actions.upload_common INFO 2016-04-14 16:47:22,521 tool upload1 created job id 1 +galaxy.tools.actions.upload DEBUG 2016-04-14 16:47:22,655 Created upload job (229.375 ms) +galaxy.tools.execute DEBUG 2016-04-14 16:47:22,655 Tool [upload1] created job [1] (710.457 ms) +galaxy.tools.execute DEBUG 2016-04-14 16:47:22,674 Executed all jobs for tool request: (759.156 ms) +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:22,708 "POST /api/tools HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:22,710 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:22,813 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:22,816 Starting new HTTP connection (1): localhost +galaxy.jobs DEBUG 2016-04-14 16:47:22,927 (1) Working directory for job is: /tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1 +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:22,959 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:22,963 Starting new HTTP connection (1): localhost +galaxy.jobs.handler DEBUG 2016-04-14 16:47:22,964 (1) Dispatching to local runner +galaxy.jobs DEBUG 2016-04-14 16:47:23,090 (1) Persisting job destination (destination id: local:///) +galaxy.jobs.runners DEBUG 2016-04-14 16:47:23,172 Job [1] queued (204.971 ms) +galaxy.jobs.handler INFO 2016-04-14 16:47:23,227 (1) Job dispatched +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:23,290 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:23,293 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:23,562 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:23,568 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:23,913 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:23,915 Starting new HTTP connection (1): localhost +galaxy.tools.deps DEBUG 2016-04-14 16:47:23,998 Building dependency shell command for dependency 'samtools' +galaxy.tools.deps DEBUG 2016-04-14 16:47:23,998 Find dependency samtools version None +galaxy.tools.deps DEBUG 2016-04-14 16:47:23,998 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-14 16:47:23,999 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-14 16:47:23,999 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-14 16:47:24,000 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) +galaxy.tools.deps DEBUG 2016-04-14 16:47:24,001 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) +galaxy.tools.deps WARNING 2016-04-14 16:47:24,001 Failed to resolve dependency on 'samtools', ignoring +galaxy.jobs.command_factory INFO 2016-04-14 16:47:24,110 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 2016-04-14 16:47:24,160 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:24,164 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:24,477 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:24,480 Starting new HTTP connection (1): localhost +galaxy.jobs.runners DEBUG 2016-04-14 16:47:24,679 (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 2016-04-14 16:47:24,695 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +galaxy.jobs.runners.local DEBUG 2016-04-14 16:47:24,698 (1) executing job script: /tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/galaxy_1.sh +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:24,704 Starting new HTTP connection (1): localhost +galaxy.jobs DEBUG 2016-04-14 16:47:24,711 (1) Persisting job destination (destination id: local:///) +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:24,969 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:24,972 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,131 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,133 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,237 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,239 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,387 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,397 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,499 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,502 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,605 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,607 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,752 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,754 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,856 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,858 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,961 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,964 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,065 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,068 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,171 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,173 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,277 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,280 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,380 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,383 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,528 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,530 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,631 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,633 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,750 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,753 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,858 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,860 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,962 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,965 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,067 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,069 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,171 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,174 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,275 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,277 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,378 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,380 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,548 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,550 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,651 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,653 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,767 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,770 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,870 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,872 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,975 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,977 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:28,080 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:28,083 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:28,184 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:28,185 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:28,287 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:28,288 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:28,400 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:28,402 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:28,504 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:28,506 Starting new HTTP connection (1): localhost +galaxy.jobs.runners.local DEBUG 2016-04-14 16:47:28,549 execution finished: /tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/galaxy_1.sh +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:28,869 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:28,871 Starting new HTTP connection (1): localhost +galaxy.datatypes.metadata DEBUG 2016-04-14 16:47:29,058 loading metadata from file for: HistoryDatasetAssociation 1 +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:29,102 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:29,105 Starting new HTTP connection (1): localhost +requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:29,415 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None +functional_tests.py INFO 2016-04-14 16:47:29,425 Shutting down +functional_tests.py INFO 2016-04-14 16:47:29,425 Shutting down embedded web server +functional_tests.py INFO 2016-04-14 16:47:29,428 Embedded web server stopped +functional_tests.py INFO 2016-04-14 16:47:29,428 Shutting down app +galaxy.jobs.handler INFO 2016-04-14 16:47:29,428 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-14 16:47:29,428 job handler queue stopped +galaxy.jobs.runners INFO 2016-04-14 16:47:29,428 TaskRunner: Sending stop signal to 2 worker threads +galaxy.jobs.runners INFO 2016-04-14 16:47:29,428 LocalRunner: Sending stop signal to 5 worker threads +galaxy.jobs.handler INFO 2016-04-14 16:47:29,429 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-14 16:47:29,429 job handler stop queue stopped +functional_tests.py INFO 2016-04-14 16:47:29,429 Embedded Universe application stopped +functional_tests.py INFO 2016-04-14 16:47:29,429 Cleaning up temporary files in /tmp/714419.1.short.q/tmp6xBwof/tmpacHkJy +galaxy.jobs DEBUG 2016-04-14 16:47:29,555 job 1 ended (finish() executed in (1006.205 ms)) +galaxy.jobs.handler INFO 2016-04-14 16:47:30,107 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-14 16:47:30,107 job handler queue stopped +galaxy.jobs.runners INFO 2016-04-14 16:47:30,107 TaskRunner: Sending stop signal to 2 worker threads +galaxy.jobs.runners INFO 2016-04-14 16:47:30,107 LocalRunner: Sending stop signal to 5 worker threads +galaxy.jobs.handler INFO 2016-04-14 16:47:30,107 sending stop signal to worker thread +galaxy.jobs.handler INFO 2016-04-14 16:47:30,107 job handler stop queue stopped testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3[0]: failed