changeset 11:d33e0ed5f32a draft

planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835-dirty
author lecorguille
date Thu, 14 Apr 2016 10:03:48 -0400
parents 01a900f2e464
children db270f704d93
files CAMERA.r abims_CAMERA_annotateDiffreport.xml qsub.err qsub.out test-data/xset.group.retcor.group.fillPeaks.RData
diffstat 5 files changed, 2426 insertions(+), 1309 deletions(-) [+]
line wrap: on
line diff
--- a/CAMERA.r	Tue Apr 12 04:11:58 2016 -0400
+++ b/CAMERA.r	Thu Apr 14 10:03:48 2016 -0400
@@ -94,14 +94,39 @@
 #Import the different functions
 source_local("lib.r")
 
+#necessary to unzip .zip file uploaded to Galaxy
+#thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories
+
+
+if (!is.null(listArguments[["zipfile"]])){
+  zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
+}
+
 # We unzip automatically the chromatograms from the zip files.
-if (thefunction == "annotatediff")  {
+if (thefunction %in% c("xcmsSet","retcor","fillPeaks"))  {
   if(exists("zipfile") && (zipfile!="")) {
+    if(!file.exists(zipfile)){
+      error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
+      print(error_message)
+      stop(error_message)
+    }
+
+    #unzip
     suppressWarnings(unzip(zipfile, unzip="unzip"))
+
+    #get the directory name
+    filesInZip=unzip(zipfile, list=T); 
+    directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
+    directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
+    directory = "."
+    if (length(directories) == 1) directory = directories
+    
+    cat("files_root_directory\t",directory,"\n")
   }
 }
 
 
+
 #addition of xset object to the list of arguments in the first position
 if (exists("xset") != 0){
   listArguments=append(list(xset), listArguments)
--- a/abims_CAMERA_annotateDiffreport.xml	Tue Apr 12 04:11:58 2016 -0400
+++ b/abims_CAMERA_annotateDiffreport.xml	Thu Apr 14 10:03:48 2016 -0400
@@ -48,7 +48,10 @@
             new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_
         #end if
         
-      
+        #if $zip_file:
+            zipfile $zip_file
+        #end if
+
     ]]></command>
 
     <inputs>
@@ -123,7 +126,9 @@
             <when value="hide">
             </when>
         </conditional>
-       
+
+        <!-- To pass planemo test -->
+        <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." />
     </inputs>
 
     <outputs>
@@ -135,9 +140,9 @@
                 <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" />
             </change_format>
         </data>
-	<data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True">
-		 <filter>(options['option'] == 'show')</filter>
-	</data>    
+        <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True">
+		        <filter>(options['option'] == 'show')</filter>
+	      </data>    
     </outputs>
     
     <tests>
@@ -171,6 +176,7 @@
             <param name="options|w" value="640"/>
             <param name="options|mzdec" value="2"/>
             <param name="options|sortpval" value="False"/>
+            <param name="zip_file" value="sacuri_dir_root.zip"  ftype="zip" />
             <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
             <output name="datamatrix" file="xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
         </test>
--- a/qsub.err	Tue Apr 12 04:11:58 2016 -0400
+++ b/qsub.err	Thu Apr 14 10:03:48 2016 -0400
@@ -20,35 +20,1112 @@
 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/713417.1.short.q/tmp32I4oD/galaxy-dev/lib, /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/lib, /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/test, /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python27.zip, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/plat-linux2, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-old, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-dynload, /opt/6.x/python-2.7.2/lib/python2.7, /opt/6.x/python-2.7.2/lib/python2.7/plat-linux2, /opt/6.x/python-2.7.2/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages
+DEBUG:galaxy.app:python path is: /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/lib, /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/lib, /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/test, /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python27.zip, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/plat-linux2, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-old, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/lib-dynload, /opt/6.x/python-2.7.2/lib/python2.7, /opt/6.x/python-2.7.2/lib/python2.7/plat-linux2, /opt/6.x/python-2.7.2/lib/python2.7/lib-tk, /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages
 INFO:galaxy.config:Logging at '10' level to 'stdout'
 /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:565: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.
   'storage.' % (dialect.name, dialect.driver))
-CAMERA.annotate ( testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 ) > Test-1 ... ERROR
+CAMERA.annotate ( testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3 ) > Test-1 ... FAIL
 
 ======================================================================
-ERROR: 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
 ----------------------------------------------------------------------
 Traceback (most recent call last):
-  File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/case.py", line 133, in run
-    self.runTest(result)
-  File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/case.py", line 151, in runTest
-    test(result)
-  File "/opt/6.x/python-2.7.2/lib/python2.7/unittest/case.py", line 391, in __call__
-    return self.run(*args, **kwds)
-  File "/opt/6.x/python-2.7.2/lib/python2.7/unittest/case.py", line 331, in run
-    result.addFailure(self, sys.exc_info())
-  File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/proxy.py", line 146, in addFailure
-    plugins.addFailure(self.test, err)
-  File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/plugins/manager.py", line 99, in __call__
-    return self.call(*arg, **kw)
-  File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nose/plugins/manager.py", line 167, in simple
-    result = meth(*arg, **kw)
-  File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nosehtml/plugin.py", line 93, in addFailure
-    self.print_test( 'failure', test, '\n'.join( traceback.format_exception( *error ) ) )
-  File "/home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages/nosehtml/plugin.py", line 67, in print_test
-    print >> f.file, "<div id='capture_%d' style='display: none'><pre class='capture'>%s</pre></div>" % ( f.counter, cgi.escape( test.capturedOutput ) )
-UnicodeEncodeError: 'ascii' codec can't encode character u'\u2018' in position 413: ordinal not in range(128)
+  File "/tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/test/functional/test_toolbox.py", line 289, in test_tool
+    self.do_it( td )
+  File "/tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/test/functional/test_toolbox.py", line 73, in do_it
+    raise e
+JobOutputsError: Job in error state.
+Job in error state.
+Job in error state.
+-------------------- >> begin captured stdout << ---------------------
+History with id 2891970512fa2d5a in error - summary of datasets in error below.
+--------------------------------------
+| 2 - xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv (HID - NAME) 
+| Dataset Blurb:
+|  error
+| Dataset Info:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj
+| Dataset Job Standard Output:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat
+|  variableMetadataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat
+|  dataMatrixOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat
+|  xsetRdataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat
+|  convert_param	FALSE
+|  num_digits	0
+|  nSlaves	1
+|  sigma	6
+|  perfwhm	0.6
+|  maxcharge	3
+|  maxiso	4
+|  minfrac	0.5
+|  ppm	5
+|  mzabs	0.015
+|  intval	into
+|  max_peaks	100
+|  quick	FALSE
+|  polarity	negative
+|  cor_eic_th	0.75
+|  graphMethod	hcs
+|  pval	0.05
+|  calcCiS	TRUE
+|  calcIso	FALSE
+|  calcCaS	FALSE
+|  multiplier	3
+|  runDiffreport	TRUE
+|  eicmax	200
+|  eicwidth	200
+|  value	into
+|  sortpval	FALSE
+|  h	480
+|  w	640
+|  mzdec	2
+|  new_file_path	/tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_
+|  INFILE PROCESSING INFO
+|  ARGUMENTS PROCESSING INFO
+|  MAIN PROCESSING INFO
+|  Start grouping after retention time.
+|  Created 1336 pseudospectra.
+|  Generating peak matrix!
+|  Run isotope peak annotation
+|  % finished: 10  20  30  40  50  60  70  80  90  100
+|  Found isotopes: 167
+|  Start grouping after correlation.
+|  Generating EIC's ..
+| Dataset Job Standard Error:
+|  Fatal error: Exit code 1 ()
+|  arguments 'minimized' and 'invisible' are for Windows only
+|  Error in getAllPeakEICs(object, index = index) :
+|  Raw data file:./sacuri/bio/HU_neg_028.mzXML not found !
+|  Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
+|  Execution halted
+|
+--------------------------------------
+| 3 - xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv (HID - NAME) 
+| Dataset Blurb:
+|  error
+| Dataset Info:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj
+| Dataset Job Standard Output:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat
+|  variableMetadataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat
+|  dataMatrixOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat
+|  xsetRdataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat
+|  convert_param	FALSE
+|  num_digits	0
+|  nSlaves	1
+|  sigma	6
+|  perfwhm	0.6
+|  maxcharge	3
+|  maxiso	4
+|  minfrac	0.5
+|  ppm	5
+|  mzabs	0.015
+|  intval	into
+|  max_peaks	100
+|  quick	FALSE
+|  polarity	negative
+|  cor_eic_th	0.75
+|  graphMethod	hcs
+|  pval	0.05
+|  calcCiS	TRUE
+|  calcIso	FALSE
+|  calcCaS	FALSE
+|  multiplier	3
+|  runDiffreport	TRUE
+|  eicmax	200
+|  eicwidth	200
+|  value	into
+|  sortpval	FALSE
+|  h	480
+|  w	640
+|  mzdec	2
+|  new_file_path	/tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_
+|  INFILE PROCESSING INFO
+|  ARGUMENTS PROCESSING INFO
+|  MAIN PROCESSING INFO
+|  Start grouping after retention time.
+|  Created 1336 pseudospectra.
+|  Generating peak matrix!
+|  Run isotope peak annotation
+|  % finished: 10  20  30  40  50  60  70  80  90  100
+|  Found isotopes: 167
+|  Start grouping after correlation.
+|  Generating EIC's ..
+| Dataset Job Standard Error:
+|  Fatal error: Exit code 1 ()
+|  arguments 'minimized' and 'invisible' are for Windows only
+|  Error in getAllPeakEICs(object, index = index) :
+|  Raw data file:./sacuri/bio/HU_neg_028.mzXML not found !
+|  Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
+|  Execution halted
+|
+--------------------------------------
+| 4 - xset.group.retcor.group.fillPeaks.annotate.negative.Rdata (HID - NAME) 
+| Dataset Blurb:
+|  error
+| Dataset Info:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj
+| Dataset Job Standard Output:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat
+|  variableMetadataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat
+|  dataMatrixOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat
+|  xsetRdataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat
+|  convert_param	FALSE
+|  num_digits	0
+|  nSlaves	1
+|  sigma	6
+|  perfwhm	0.6
+|  maxcharge	3
+|  maxiso	4
+|  minfrac	0.5
+|  ppm	5
+|  mzabs	0.015
+|  intval	into
+|  max_peaks	100
+|  quick	FALSE
+|  polarity	negative
+|  cor_eic_th	0.75
+|  graphMethod	hcs
+|  pval	0.05
+|  calcCiS	TRUE
+|  calcIso	FALSE
+|  calcCaS	FALSE
+|  multiplier	3
+|  runDiffreport	TRUE
+|  eicmax	200
+|  eicwidth	200
+|  value	into
+|  sortpval	FALSE
+|  h	480
+|  w	640
+|  mzdec	2
+|  new_file_path	/tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_
+|  INFILE PROCESSING INFO
+|  ARGUMENTS PROCESSING INFO
+|  MAIN PROCESSING INFO
+|  Start grouping after retention time.
+|  Created 1336 pseudospectra.
+|  Generating peak matrix!
+|  Run isotope peak annotation
+|  % finished: 10  20  30  40  50  60  70  80  90  100
+|  Found isotopes: 167
+|  Start grouping after correlation.
+|  Generating EIC's ..
+| Dataset Job Standard Error:
+|  Fatal error: Exit code 1 ()
+|  arguments 'minimized' and 'invisible' are for Windows only
+|  Error in getAllPeakEICs(object, index = index) :
+|  Raw data file:./sacuri/bio/HU_neg_028.mzXML not found !
+|  Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
+|  Execution halted
+|
+--------------------------------------
+| 5 - xset.group.retcor.group.fillPeaks.annotateDiffreport (HID - NAME) 
+| Dataset Blurb:
+|  error
+| Dataset Info:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj
+| Dataset Job Standard Output:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat
+|  variableMetadataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat
+|  dataMatrixOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat
+|  xsetRdataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat
+|  convert_param	FALSE
+|  num_digits	0
+|  nSlaves	1
+|  sigma	6
+|  perfwhm	0.6
+|  maxcharge	3
+|  maxiso	4
+|  minfrac	0.5
+|  ppm	5
+|  mzabs	0.015
+|  intval	into
+|  max_peaks	100
+|  quick	FALSE
+|  polarity	negative
+|  cor_eic_th	0.75
+|  graphMethod	hcs
+|  pval	0.05
+|  calcCiS	TRUE
+|  calcIso	FALSE
+|  calcCaS	FALSE
+|  multiplier	3
+|  runDiffreport	TRUE
+|  eicmax	200
+|  eicwidth	200
+|  value	into
+|  sortpval	FALSE
+|  h	480
+|  w	640
+|  mzdec	2
+|  new_file_path	/tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_
+|  INFILE PROCESSING INFO
+|  ARGUMENTS PROCESSING INFO
+|  MAIN PROCESSING INFO
+|  Start grouping after retention time.
+|  Created 1336 pseudospectra.
+|  Generating peak matrix!
+|  Run isotope peak annotation
+|  % finished: 10  20  30  40  50  60  70  80  90  100
+|  Found isotopes: 167
+|  Start grouping after correlation.
+|  Generating EIC's ..
+| Dataset Job Standard Error:
+|  Fatal error: Exit code 1 ()
+|  arguments 'minimized' and 'invisible' are for Windows only
+|  Error in getAllPeakEICs(object, index = index) :
+|  Raw data file:./sacuri/bio/HU_neg_028.mzXML not found !
+|  Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
+|  Execution halted
+|
+--------------------------------------
+History with id 2891970512fa2d5a in error - summary of datasets in error below.
+--------------------------------------
+| 2 - xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv (HID - NAME) 
+| Dataset Blurb:
+|  error
+| Dataset Info:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj
+| Dataset Job Standard Output:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat
+|  variableMetadataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat
+|  dataMatrixOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat
+|  xsetRdataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat
+|  convert_param	FALSE
+|  num_digits	0
+|  nSlaves	1
+|  sigma	6
+|  perfwhm	0.6
+|  maxcharge	3
+|  maxiso	4
+|  minfrac	0.5
+|  ppm	5
+|  mzabs	0.015
+|  intval	into
+|  max_peaks	100
+|  quick	FALSE
+|  polarity	negative
+|  cor_eic_th	0.75
+|  graphMethod	hcs
+|  pval	0.05
+|  calcCiS	TRUE
+|  calcIso	FALSE
+|  calcCaS	FALSE
+|  multiplier	3
+|  runDiffreport	TRUE
+|  eicmax	200
+|  eicwidth	200
+|  value	into
+|  sortpval	FALSE
+|  h	480
+|  w	640
+|  mzdec	2
+|  new_file_path	/tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_
+|  INFILE PROCESSING INFO
+|  ARGUMENTS PROCESSING INFO
+|  MAIN PROCESSING INFO
+|  Start grouping after retention time.
+|  Created 1336 pseudospectra.
+|  Generating peak matrix!
+|  Run isotope peak annotation
+|  % finished: 10  20  30  40  50  60  70  80  90  100
+|  Found isotopes: 167
+|  Start grouping after correlation.
+|  Generating EIC's ..
+| Dataset Job Standard Error:
+|  Fatal error: Exit code 1 ()
+|  arguments 'minimized' and 'invisible' are for Windows only
+|  Error in getAllPeakEICs(object, index = index) :
+|  Raw data file:./sacuri/bio/HU_neg_028.mzXML not found !
+|  Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
+|  Execution halted
+|
+--------------------------------------
+| 3 - xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv (HID - NAME) 
+| Dataset Blurb:
+|  error
+| Dataset Info:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj
+| Dataset Job Standard Output:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat
+|  variableMetadataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat
+|  dataMatrixOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat
+|  xsetRdataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat
+|  convert_param	FALSE
+|  num_digits	0
+|  nSlaves	1
+|  sigma	6
+|  perfwhm	0.6
+|  maxcharge	3
+|  maxiso	4
+|  minfrac	0.5
+|  ppm	5
+|  mzabs	0.015
+|  intval	into
+|  max_peaks	100
+|  quick	FALSE
+|  polarity	negative
+|  cor_eic_th	0.75
+|  graphMethod	hcs
+|  pval	0.05
+|  calcCiS	TRUE
+|  calcIso	FALSE
+|  calcCaS	FALSE
+|  multiplier	3
+|  runDiffreport	TRUE
+|  eicmax	200
+|  eicwidth	200
+|  value	into
+|  sortpval	FALSE
+|  h	480
+|  w	640
+|  mzdec	2
+|  new_file_path	/tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_
+|  INFILE PROCESSING INFO
+|  ARGUMENTS PROCESSING INFO
+|  MAIN PROCESSING INFO
+|  Start grouping after retention time.
+|  Created 1336 pseudospectra.
+|  Generating peak matrix!
+|  Run isotope peak annotation
+|  % finished: 10  20  30  40  50  60  70  80  90  100
+|  Found isotopes: 167
+|  Start grouping after correlation.
+|  Generating EIC's ..
+| Dataset Job Standard Error:
+|  Fatal error: Exit code 1 ()
+|  arguments 'minimized' and 'invisible' are for Windows only
+|  Error in getAllPeakEICs(object, index = index) :
+|  Raw data file:./sacuri/bio/HU_neg_028.mzXML not found !
+|  Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
+|  Execution halted
+|
+--------------------------------------
+| 4 - xset.group.retcor.group.fillPeaks.annotate.negative.Rdata (HID - NAME) 
+| Dataset Blurb:
+|  error
+| Dataset Info:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj
+| Dataset Job Standard Output:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat
+|  variableMetadataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat
+|  dataMatrixOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat
+|  xsetRdataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat
+|  convert_param	FALSE
+|  num_digits	0
+|  nSlaves	1
+|  sigma	6
+|  perfwhm	0.6
+|  maxcharge	3
+|  maxiso	4
+|  minfrac	0.5
+|  ppm	5
+|  mzabs	0.015
+|  intval	into
+|  max_peaks	100
+|  quick	FALSE
+|  polarity	negative
+|  cor_eic_th	0.75
+|  graphMethod	hcs
+|  pval	0.05
+|  calcCiS	TRUE
+|  calcIso	FALSE
+|  calcCaS	FALSE
+|  multiplier	3
+|  runDiffreport	TRUE
+|  eicmax	200
+|  eicwidth	200
+|  value	into
+|  sortpval	FALSE
+|  h	480
+|  w	640
+|  mzdec	2
+|  new_file_path	/tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_
+|  INFILE PROCESSING INFO
+|  ARGUMENTS PROCESSING INFO
+|  MAIN PROCESSING INFO
+|  Start grouping after retention time.
+|  Created 1336 pseudospectra.
+|  Generating peak matrix!
+|  Run isotope peak annotation
+|  % finished: 10  20  30  40  50  60  70  80  90  100
+|  Found isotopes: 167
+|  Start grouping after correlation.
+|  Generating EIC's ..
+| Dataset Job Standard Error:
+|  Fatal error: Exit code 1 ()
+|  arguments 'minimized' and 'invisible' are for Windows only
+|  Error in getAllPeakEICs(object, index = index) :
+|  Raw data file:./sacuri/bio/HU_neg_028.mzXML not found !
+|  Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
+|  Execution halted
+|
+--------------------------------------
+| 5 - xset.group.retcor.group.fillPeaks.annotateDiffreport (HID - NAME) 
+| Dataset Blurb:
+|  error
+| Dataset Info:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj
+| Dataset Job Standard Output:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat
+|  variableMetadataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat
+|  dataMatrixOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat
+|  xsetRdataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat
+|  convert_param	FALSE
+|  num_digits	0
+|  nSlaves	1
+|  sigma	6
+|  perfwhm	0.6
+|  maxcharge	3
+|  maxiso	4
+|  minfrac	0.5
+|  ppm	5
+|  mzabs	0.015
+|  intval	into
+|  max_peaks	100
+|  quick	FALSE
+|  polarity	negative
+|  cor_eic_th	0.75
+|  graphMethod	hcs
+|  pval	0.05
+|  calcCiS	TRUE
+|  calcIso	FALSE
+|  calcCaS	FALSE
+|  multiplier	3
+|  runDiffreport	TRUE
+|  eicmax	200
+|  eicwidth	200
+|  value	into
+|  sortpval	FALSE
+|  h	480
+|  w	640
+|  mzdec	2
+|  new_file_path	/tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_
+|  INFILE PROCESSING INFO
+|  ARGUMENTS PROCESSING INFO
+|  MAIN PROCESSING INFO
+|  Start grouping after retention time.
+|  Created 1336 pseudospectra.
+|  Generating peak matrix!
+|  Run isotope peak annotation
+|  % finished: 10  20  30  40  50  60  70  80  90  100
+|  Found isotopes: 167
+|  Start grouping after correlation.
+|  Generating EIC's ..
+| Dataset Job Standard Error:
+|  Fatal error: Exit code 1 ()
+|  arguments 'minimized' and 'invisible' are for Windows only
+|  Error in getAllPeakEICs(object, index = index) :
+|  Raw data file:./sacuri/bio/HU_neg_028.mzXML not found !
+|  Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
+|  Execution halted
+|
+--------------------------------------
+History with id 2891970512fa2d5a in error - summary of datasets in error below.
+--------------------------------------
+| 2 - xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv (HID - NAME) 
+| Dataset Blurb:
+|  error
+| Dataset Info:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj
+| Dataset Job Standard Output:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat
+|  variableMetadataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat
+|  dataMatrixOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat
+|  xsetRdataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat
+|  convert_param	FALSE
+|  num_digits	0
+|  nSlaves	1
+|  sigma	6
+|  perfwhm	0.6
+|  maxcharge	3
+|  maxiso	4
+|  minfrac	0.5
+|  ppm	5
+|  mzabs	0.015
+|  intval	into
+|  max_peaks	100
+|  quick	FALSE
+|  polarity	negative
+|  cor_eic_th	0.75
+|  graphMethod	hcs
+|  pval	0.05
+|  calcCiS	TRUE
+|  calcIso	FALSE
+|  calcCaS	FALSE
+|  multiplier	3
+|  runDiffreport	TRUE
+|  eicmax	200
+|  eicwidth	200
+|  value	into
+|  sortpval	FALSE
+|  h	480
+|  w	640
+|  mzdec	2
+|  new_file_path	/tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_
+|  INFILE PROCESSING INFO
+|  ARGUMENTS PROCESSING INFO
+|  MAIN PROCESSING INFO
+|  Start grouping after retention time.
+|  Created 1336 pseudospectra.
+|  Generating peak matrix!
+|  Run isotope peak annotation
+|  % finished: 10  20  30  40  50  60  70  80  90  100
+|  Found isotopes: 167
+|  Start grouping after correlation.
+|  Generating EIC's ..
+| Dataset Job Standard Error:
+|  Fatal error: Exit code 1 ()
+|  arguments 'minimized' and 'invisible' are for Windows only
+|  Error in getAllPeakEICs(object, index = index) :
+|  Raw data file:./sacuri/bio/HU_neg_028.mzXML not found !
+|  Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
+|  Execution halted
+|
+--------------------------------------
+| 3 - xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv (HID - NAME) 
+| Dataset Blurb:
+|  error
+| Dataset Info:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj
+| Dataset Job Standard Output:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat
+|  variableMetadataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat
+|  dataMatrixOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat
+|  xsetRdataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat
+|  convert_param	FALSE
+|  num_digits	0
+|  nSlaves	1
+|  sigma	6
+|  perfwhm	0.6
+|  maxcharge	3
+|  maxiso	4
+|  minfrac	0.5
+|  ppm	5
+|  mzabs	0.015
+|  intval	into
+|  max_peaks	100
+|  quick	FALSE
+|  polarity	negative
+|  cor_eic_th	0.75
+|  graphMethod	hcs
+|  pval	0.05
+|  calcCiS	TRUE
+|  calcIso	FALSE
+|  calcCaS	FALSE
+|  multiplier	3
+|  runDiffreport	TRUE
+|  eicmax	200
+|  eicwidth	200
+|  value	into
+|  sortpval	FALSE
+|  h	480
+|  w	640
+|  mzdec	2
+|  new_file_path	/tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_
+|  INFILE PROCESSING INFO
+|  ARGUMENTS PROCESSING INFO
+|  MAIN PROCESSING INFO
+|  Start grouping after retention time.
+|  Created 1336 pseudospectra.
+|  Generating peak matrix!
+|  Run isotope peak annotation
+|  % finished: 10  20  30  40  50  60  70  80  90  100
+|  Found isotopes: 167
+|  Start grouping after correlation.
+|  Generating EIC's ..
+| Dataset Job Standard Error:
+|  Fatal error: Exit code 1 ()
+|  arguments 'minimized' and 'invisible' are for Windows only
+|  Error in getAllPeakEICs(object, index = index) :
+|  Raw data file:./sacuri/bio/HU_neg_028.mzXML not found !
+|  Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
+|  Execution halted
+|
+--------------------------------------
+| 4 - xset.group.retcor.group.fillPeaks.annotate.negative.Rdata (HID - NAME) 
+| Dataset Blurb:
+|  error
+| Dataset Info:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj
+| Dataset Job Standard Output:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat
+|  variableMetadataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat
+|  dataMatrixOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat
+|  xsetRdataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat
+|  convert_param	FALSE
+|  num_digits	0
+|  nSlaves	1
+|  sigma	6
+|  perfwhm	0.6
+|  maxcharge	3
+|  maxiso	4
+|  minfrac	0.5
+|  ppm	5
+|  mzabs	0.015
+|  intval	into
+|  max_peaks	100
+|  quick	FALSE
+|  polarity	negative
+|  cor_eic_th	0.75
+|  graphMethod	hcs
+|  pval	0.05
+|  calcCiS	TRUE
+|  calcIso	FALSE
+|  calcCaS	FALSE
+|  multiplier	3
+|  runDiffreport	TRUE
+|  eicmax	200
+|  eicwidth	200
+|  value	into
+|  sortpval	FALSE
+|  h	480
+|  w	640
+|  mzdec	2
+|  new_file_path	/tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_
+|  INFILE PROCESSING INFO
+|  ARGUMENTS PROCESSING INFO
+|  MAIN PROCESSING INFO
+|  Start grouping after retention time.
+|  Created 1336 pseudospectra.
+|  Generating peak matrix!
+|  Run isotope peak annotation
+|  % finished: 10  20  30  40  50  60  70  80  90  100
+|  Found isotopes: 167
+|  Start grouping after correlation.
+|  Generating EIC's ..
+| Dataset Job Standard Error:
+|  Fatal error: Exit code 1 ()
+|  arguments 'minimized' and 'invisible' are for Windows only
+|  Error in getAllPeakEICs(object, index = index) :
+|  Raw data file:./sacuri/bio/HU_neg_028.mzXML not found !
+|  Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
+|  Execution halted
+|
+--------------------------------------
+| 5 - xset.group.retcor.group.fillPeaks.annotateDiffreport (HID - NAME) 
+| Dataset Blurb:
+|  error
+| Dataset Info:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj
+| Dataset Job Standard Output:
+|  PACKAGE INFO
+|  parallel	3.1.2
+|  BiocGenerics	0.14.0
+|  Biobase	2.28.0
+|  Rcpp	0.12.0
+|  mzR	2.2.2
+|  tcltk	3.1.2
+|  igraph	0.7.1
+|  xcms	1.44.0
+|  snow	0.3.13
+|  CAMERA	1.22.0
+|  multtest	2.22.0
+|  batch	1.1.4
+|  ARGUMENTS INFO
+|  xfunction	annotatediff
+|  image	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat
+|  variableMetadataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat
+|  dataMatrixOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat
+|  xsetRdataOutput	/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat
+|  convert_param	FALSE
+|  num_digits	0
+|  nSlaves	1
+|  sigma	6
+|  perfwhm	0.6
+|  maxcharge	3
+|  maxiso	4
+|  minfrac	0.5
+|  ppm	5
+|  mzabs	0.015
+|  intval	into
+|  max_peaks	100
+|  quick	FALSE
+|  polarity	negative
+|  cor_eic_th	0.75
+|  graphMethod	hcs
+|  pval	0.05
+|  calcCiS	TRUE
+|  calcIso	FALSE
+|  calcCaS	FALSE
+|  multiplier	3
+|  runDiffreport	TRUE
+|  eicmax	200
+|  eicwidth	200
+|  value	into
+|  sortpval	FALSE
+|  h	480
+|  w	640
+|  mzdec	2
+|  new_file_path	/tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_
+|  INFILE PROCESSING INFO
+|  ARGUMENTS PROCESSING INFO
+|  MAIN PROCESSING INFO
+|  Start grouping after retention time.
+|  Created 1336 pseudospectra.
+|  Generating peak matrix!
+|  Run isotope peak annotation
+|  % finished: 10  20  30  40  50  60  70  80  90  100
+|  Found isotopes: 167
+|  Start grouping after correlation.
+|  Generating EIC's ..
+| Dataset Job Standard Error:
+|  Fatal error: Exit code 1 ()
+|  arguments 'minimized' and 'invisible' are for Windows only
+|  Error in getAllPeakEICs(object, index = index) :
+|  Raw data file:./sacuri/bio/HU_neg_028.mzXML not found !
+|  Calls: annotatediff ... groupCorr -> .local -> getAllPeakEICs -> getAllPeakEICs
+|  Execution halted
+|
+--------------------------------------
+
+--------------------- >> end captured stdout << ----------------------
 -------------------- >> begin captured logging << --------------------
 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
 galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key
@@ -62,192 +1139,197 @@
 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 (18.524 ms)
-galaxy.tools.actions.upload: DEBUG: Persisted uploads (20.819 ms)
-galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (421.017 ms)
+galaxy.tools: DEBUG: Validated and populated state for tool request (19.760 ms)
+galaxy.tools.actions.upload: DEBUG: Persisted uploads (22.581 ms)
+galaxy.tools.actions.upload: DEBUG: Checked and cleaned uploads (487.187 ms)
 galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1
-galaxy.tools.actions.upload: DEBUG: Created upload job (212.151 ms)
-galaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (654.615 ms)
-galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (699.689 ms)
+galaxy.tools.actions.upload: DEBUG: Created upload job (242.417 ms)
+galaxy.tools.execute: DEBUG: Tool [upload1] created job [1] (752.711 ms)
+galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (795.117 ms)
 requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None
 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None
+requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
+requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None
+requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
+requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None
 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
-galaxy.jobs: DEBUG: (1) Working directory for job is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1
+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
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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 (144.152 ms)
+galaxy.jobs.runners: DEBUG: Job [1] queued (194.097 ms)
 galaxy.jobs.handler: INFO: (1) Job dispatched
-requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None
 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
 galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools'
 galaxy.tools.deps: DEBUG: Find dependency samtools version None
-galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
+galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True)
+galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True)
+galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True)
+galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True)
+galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True)
+requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None
 galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring
-requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d 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: INFO: Starting new HTTP connection (1): localhost
-galaxy.jobs.command_factory: INFO: Built script [/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/tools/data_source/upload.py /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev /tmp/713417.1.short.q/tmp32I4oD/tmp/tmpIuu2Wr /tmp/713417.1.short.q/tmp32I4oD/tmp/tmpKio67E 1:/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/dataset_1_files:/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_1.dat]
-requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None
 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
-galaxy.jobs.runners: DEBUG: (1) command is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/set_metadata_aCYbsb.py" "/tmp/713417.1.short.q/tmp32I4oD/tmp/tmpIuu2Wr" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/galaxy.json" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_XozciK,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_PCVo6A,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_POL2Ze,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_3vJ9WJ,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_1.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_hQCXbL" 5242880; sh -c "exit $return_code"
-galaxy.jobs.runners.local: DEBUG: (1) executing job script: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/galaxy_1.sh
+galaxy.jobs.runners: DEBUG: (1) command is: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/tool_script.sh; return_code=$?; 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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None
+galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/galaxy_1.sh
 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
-galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/galaxy_1.sh
-requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None
 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
 galaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 1
-requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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 (99.599 ms)
-galaxy.jobs: DEBUG: job 1 ended (finish() executed in (864.203 ms))
-galaxy.tools.actions: INFO: Handled output (134.928 ms)
-galaxy.tools.actions: INFO: Handled output (71.983 ms)
-galaxy.tools.actions: INFO: Handled output (90.651 ms)
-galaxy.tools.actions: INFO: Handled output (90.794 ms)
-galaxy.tools.actions: INFO: Verified access to datasets (8.282 ms)
-galaxy.tools.execute: DEBUG: Tool [testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] created job [2] (601.149 ms)
-galaxy.tools.execute: DEBUG: Executed all jobs for tool request: (646.356 ms)
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-galaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2
+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:///)
-galaxy.jobs.runners: DEBUG: Job [2] queued (106.028 ms)
 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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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 0x2ac7e450d110> (isnull? False)
+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 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
+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 1.44.0
-galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: WARNING: Failed to resolve dependency on 'bioconductor-camera', ignoring
+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 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps: DEBUG: Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
+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 0x2ac83c0d9a50> (isnull? False)
+galaxy.tools.deps: DEBUG: Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b7ec80fead0> (isnull? False)
+requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
+galaxy.jobs.command_factory: INFO: Built script [/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/714401.1.short.q/tmpAQxCGj/deps/R/3.1.2/lecorguille/camera_annotate/01a900f2e464; export PACKAGE_BASE; . /tmp/714401.1.short.q/tmpAQxCGj/deps/R/3.1.2/lecorguille/camera_annotate/01a900f2e464/env.sh; PACKAGE_BASE=/tmp/714401.1.short.q/tmpAQxCGj/deps/bioconductor-camera/1.22.0/lecorguille/camera_annotate/01a900f2e464; export PACKAGE_BASE; . /tmp/714401.1.short.q/tmpAQxCGj/deps/bioconductor-camera/1.22.0/lecorguille/camera_annotate/01a900f2e464/env.sh; PACKAGE_BASE=/tmp/714401.1.short.q/tmpAQxCGj/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/01a900f2e464; export PACKAGE_BASE; . /tmp/714401.1.short.q/tmpAQxCGj/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/01a900f2e464/env.sh; LANG=C Rscript /tmp/714401.1.short.q/tmpAQxCGj/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/01a900f2e464/camera_annotate/CAMERA.r  xfunction annotatediff image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat  variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat  convert_param FALSE num_digits 0 nSlaves ${GALAXY_SLOTS:-1} sigma 6 perfwhm 0.6 maxcharge 3 maxiso 4 minfrac 0.5 ppm 5 mzabs 0.015 intval into max_peaks 100 quick FALSE polarity negative cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE multiplier 3  runDiffreport TRUE eicmax 200 eicwidth 200 value into sortpval FALSE h 480 w 640 mzdec 2 new_file_path /tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_]
+requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None
 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost
-galaxy.jobs.command_factory: INFO: Built script [/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/713417.1.short.q/tmp32I4oD/deps/R/3.1.2/lecorguille/camera_annotate/c02d80efba80; export PACKAGE_BASE; . /tmp/713417.1.short.q/tmp32I4oD/deps/R/3.1.2/lecorguille/camera_annotate/c02d80efba80/env.sh; PACKAGE_BASE=/tmp/713417.1.short.q/tmp32I4oD/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/c02d80efba80; export PACKAGE_BASE; . /tmp/713417.1.short.q/tmp32I4oD/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/c02d80efba80/env.sh; LANG=C Rscript /tmp/713417.1.short.q/tmp32I4oD/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/c02d80efba80/camera_annotate/CAMERA.r  xfunction annotatediff image /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_1.dat  variableMetadataOutput /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_2.dat dataMatrixOutput /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_3.dat xsetRdataOutput /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_4.dat  convert_param FALSE num_digits 0 nSlaves ${GALAXY_SLOTS:-1} sigma 6 perfwhm 0.6 maxcharge 3 maxiso 4 minfrac 0.5 ppm 5 mzabs 0.015 intval into max_peaks 100 quick FALSE polarity negative cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE multiplier 3  runDiffreport TRUE eicmax 200 eicwidth 200 value into sortpval FALSE h 480 w 640 mzdec 2 new_file_path /tmp/713417.1.short.q/tmp32I4oD/tmp/primary_5_]
-requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-galaxy.jobs.runners: DEBUG: (2) command is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/tool_script.sh; return_code=$?; python "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/set_metadata_7oSiGt.py" "/tmp/713417.1.short.q/tmp32I4oD/tmp/tmpIuu2Wr" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/galaxy.json" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_yQypOr,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_5pYigd,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_dqnE6s,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_bb9G1l,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_2.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_qGNTro" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_3_GFPZBf,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_3_dzMzqz,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_3_YTXBdt,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_3_60vr5_,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_3.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_3_CF9v7P" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_4_dtyp5t,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_4_0jY9lR,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_4_IYAPP7,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_4_g18Jla,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_4.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_4_YPXaBQ" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_5_w61b96,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_5_oh73F9,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_5_jXk9Pn,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_5_GgatPH,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_5.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_5_lY8WCQ" 5242880; sh -c "exit $return_code"
-galaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/galaxy_2.sh
+galaxy.jobs.runners: DEBUG: (2) command is: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/tool_script.sh; return_code=$?; 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: INFO: Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d 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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/galaxy_2.sh
+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 (651.127 ms))
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+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=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
+requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None
 --------------------- >> end captured logging << ---------------------
 
 ----------------------------------------------------------------------
-XML: /tmp/713417.1.short.q/tmp32I4oD/xunit.xml
+XML: /tmp/714401.1.short.q/tmpAQxCGj/xunit.xml
 ----------------------------------------------------------------------
-Ran 1 test in 20.783s
+Ran 1 test in 40.033s
 
-FAILED (errors=1)
-cp: cannot stat `/tmp/713417.1.short.q/tmp32I4oD/jobfiles/*': No such file or directory
-There were problems with 2 test(s) - out of 2 test(s) executed. See /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.html for detailed breakdown.
+FAILED (failures=1)
+cp: cannot stat `/tmp/714401.1.short.q/tmpAQxCGj/jobfiles/*': No such file or directory
+There were problems with 1 test(s) - out of 1 test(s) executed. See /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.html for detailed breakdown.
--- a/qsub.out	Tue Apr 12 04:11:58 2016 -0400
+++ b/qsub.out	Thu Apr 14 10:03:48 2016 -0400
@@ -1,6 +1,6 @@
 git --git-dir /home/fr2424/sib/lecorguille/.planemo/gx_repo fetch >/dev/null 2>&1
-cd /tmp/713417.1.short.q/tmp32I4oD; 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/713417.1.short.q/tmp32I4oD/galaxy-dev/.git/
+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/
 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/713417.1.short.q/tmp32I4oD/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/713417.1.short.q/tmp32I4oD/galaxy-dev/run.sh $COMMON_STARTUP_ARGS --daemon --wait]
+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]
 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/713417.1.short.q/tmp32I4oD/galaxy-dev
-Testing tools with command [cd /tmp/713417.1.short.q/tmp32I4oD/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/713417.1.short.q/tmp32I4oD/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/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]
 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
@@ -197,1173 +197,1177 @@
 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/713417.1.short.q/tmpqY2f0s/tmpcxO90Y/new_files_path_HU_Ghg'), ('app:main', 'database_connection', 'sqlite:////tmp/713417.1.short.q/tmpqY2f0s/tmpcxO90Y/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/713417.1.short.q/tmpxaLrzG'), ('app:main', 'template_cache_path', '/tmp/713417.1.short.q/tmpqY2f0s/tmpcxO90Y/database/compiled_templates'), ('app:main', 'job_working_directory', '/tmp/713417.1.short.q/tmpqY2f0s/tmpcxO90Y/job_working_directory_57dU3e'), ('app:main', 'tool_dependency_dir', '/tmp/713417.1.short.q/tmp32I4oD/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/713417.1.short.q/tmpqY2f0s/data_manager_test_tmpyMBM1q/data_manager_tool-dataLuK1sc'), ('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/713417.1.short.q/tmpqY2f0s/tmpcxO90Y/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 2016-04-11 17:47:07,898 Initalizing main Galaxy Queue Worker on sqlalchemy+sqlite://
-tool_shed.tool_shed_registry DEBUG 2016-04-11 17:47:07,941 Loading references to tool sheds from /tmp/713417.1.short.q/tmp32I4oD/tool_sheds_conf.xml
-tool_shed.tool_shed_registry DEBUG 2016-04-11 17:47:07,941 Loaded reference to tool shed: Target Shed
-galaxy.app DEBUG 2016-04-11 17:47:07,942 Using "galaxy.ini" config file: /tmp/713417.1.short.q/tmpqY2f0s/functional_tests_wsgi.ini
-migrate.versioning.repository DEBUG 2016-04-11 17:47:08,017 Loading repository lib/galaxy/model/migrate...
-migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py...
-migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully
-migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py...
-migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully
-migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py...
-migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully
-migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py...
-migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,018 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully
-migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,019 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py...
-migrate.versioning.script.base DEBUG 2016-04-11 17:47:08,019 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully
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-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,159 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,160 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,161 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,161 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,161 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,161 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,162 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,163 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,165 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,165 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,165 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,166 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,167 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,168 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,169 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,170 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,171 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,172 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,173 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,174 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,175 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,175 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,175 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,175 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,175 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,175 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,176 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,176 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,176 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,178 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,178 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,178 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,178 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,178 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,178 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,179 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,180 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,180 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,180 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,180 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,180 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,181 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,182 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,182 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,183 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,183 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,183 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,183 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,183 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,184 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,184 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,184 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,184 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,184 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,184 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,185 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,185 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,185 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,185 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,185 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,185 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,187 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,189 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,189 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,189 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,189 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,189 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,189 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,194 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,194 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,194 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,194 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,194 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,194 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,196 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,196 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,196 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,196 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,196 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,196 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,200 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,200 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Overriding conflicting datatype with extension 'rdata', using datatype from ./config/datatypes_conf.xml.sample.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,201 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,202 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,202 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,203 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,203 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,203 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,203 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,203 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,203 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:MzSQlite'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,204 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:IdpDB'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:SQlite'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:H5'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Bam'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Sff'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,205 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,206 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Removed conflicting sniffer for datatype 'galaxy.datatypes.xml:GenericXml'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,207 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Maf'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Lav'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:csFasta'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fasta'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fastq'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Wiggle'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,208 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Removed conflicting sniffer for datatype 'galaxy.datatypes.images:Html'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.images:Html'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Axt'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Bed'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gtf'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,209 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff3'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Pileup'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Interval'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Sam'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,210 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.text:Json'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:CSV'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,211 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Png'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Im'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,212 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,213 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,214 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,215 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 2016-04-11 17:47:08,215 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,215 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,215 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:08,215 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt
-galaxy.jobs WARNING 2016-04-11 17:47:08,274 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/713417.1.short.q/tmpqY2f0s/functional_tests_wsgi.ini" instead
-galaxy.jobs DEBUG 2016-04-11 17:47:08,274 Loading job configuration from /tmp/713417.1.short.q/tmpqY2f0s/functional_tests_wsgi.ini
-galaxy.jobs DEBUG 2016-04-11 17:47:08,274 Done loading job configuration
-beaker.container DEBUG 2016-04-11 17:47:08,302 data file /tmp/713417.1.short.q/tmp32I4oD/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache
-galaxy.tools.toolbox.watcher INFO 2016-04-11 17:47:08,303 Watchdog library unavailble, cannot monitor tools.
-galaxy.tools.toolbox.base INFO 2016-04-11 17:47:08,303 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/tool_conf.xml
-galaxy.tools.toolbox.base INFO 2016-04-11 17:47:08,314 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/config/shed_tool_conf.xml
-galaxy.tools.toolbox.base INFO 2016-04-11 17:47:08,352 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/empty_tool_conf.xml
-galaxy.tools.toolbox.base DEBUG 2016-04-11 17:47:08,356 Loaded tool id: upload1, version: 1.1.4 into tool panel..
-galaxy.tools.toolbox.base DEBUG 2016-04-11 17:47:08,356 Loading section: Shed Installs
-galaxy.tools.toolbox.base DEBUG 2016-04-11 17:47:08,541 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 2016-04-11 17:47:08,543 Unable to find config file './dependency_resolvers_conf.xml'
-galaxy.tools.search DEBUG 2016-04-11 17:47:08,618 Starting to build toolbox index.
-galaxy.tools.search DEBUG 2016-04-11 17:47:09,023 Toolbox index finished.
-galaxy.tools.data_manager.manager DEBUG 2016-04-11 17:47:09,026 Loaded Data Manager: test_data_manager
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,029 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,032 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False.
-galaxy.datatypes.display_applications.application ERROR 2016-04-11 17:47:09,034 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,034 Loaded display application 'igv_bam' for datatype 'bam', inherit=False.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,035 Loaded display application 'igb_bam' for datatype 'bam', inherit=False.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,035 Loaded display application 'igb_bed' for datatype 'bed', inherit=False.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,036 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,038 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,039 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,042 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,042 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,048 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True.
-galaxy.datatypes.display_applications.application ERROR 2016-04-11 17:47:09,051 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,051 Loaded display application 'igv_gff' for datatype 'gff', inherit=True.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,051 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,058 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,067 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,068 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True.
-galaxy.datatypes.display_applications.application ERROR 2016-04-11 17:47:09,071 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,071 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,073 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,076 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False.
-galaxy.datatypes.display_applications.application ERROR 2016-04-11 17:47:09,078 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,079 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,080 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,080 Loaded display application 'igb_wig' for datatype 'wig', inherit=False.
-galaxy.datatypes.display_applications.application ERROR 2016-04-11 17:47:09,083 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,083 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False.
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,083 Adding inherited display application 'ensembl_gff' to datatype 'gtf'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,083 Adding inherited display application 'igv_gff' to datatype 'gtf'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,084 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,084 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,084 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,084 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,084 Adding inherited display application 'ensembl_interval' to datatype 'bed12'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,084 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,085 Adding inherited display application 'rviewer_interval' to datatype 'bed12'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,085 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,085 Adding inherited display application 'ensembl_interval' to datatype 'chrint'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,085 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,085 Adding inherited display application 'rviewer_interval' to datatype 'chrint'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,085 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,086 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,086 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,086 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,086 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'ensembl_interval' to datatype 'bed'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'rviewer_interval' to datatype 'bed'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,087 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,088 Adding inherited display application 'ensembl_gff' to datatype 'gff3'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,088 Adding inherited display application 'igv_gff' to datatype 'gff3'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,088 Adding inherited display application 'ensembl_interval' to datatype 'bed6'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,088 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,088 Adding inherited display application 'rviewer_interval' to datatype 'bed6'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,088 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6'
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,090 Loaded converter: CONVERTER_Bam_Bai_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,091 Loaded converter: CONVERTER_bam_to_bigwig_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,092 Loaded converter: CONVERTER_bed_to_gff_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,093 Loaded converter: CONVERTER_bed_to_bgzip_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,094 Loaded converter: CONVERTER_bed_to_tabix_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,095 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,096 Loaded converter: CONVERTER_bed_to_fli_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,097 Loaded converter: CONVERTER_bedgraph_to_bigwig
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,098 Loaded converter: CONVERTER_len_to_linecount
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,099 Loaded converter: CONVERTER_interval_to_bgzip_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,101 Loaded converter: CONVERTER_interval_to_tabix_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,102 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,103 Loaded converter: CONVERTER_fasta_to_tabular
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,104 Loaded converter: CONVERTER_fasta_to_bowtie_base_index
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,105 Loaded converter: CONVERTER_fasta_to_bowtie_color_index
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,106 Loaded converter: CONVERTER_fasta_to_2bit
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,107 Loaded converter: CONVERTER_fasta_to_len
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,108 Loaded converter: CONVERTER_fastq_to_fqtoc0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,109 Loaded converter: CONVERTER_fastq_to_fqtoc0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,110 Loaded converter: CONVERTER_fastq_to_fqtoc0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,111 Loaded converter: CONVERTER_fastq_to_fqtoc0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,112 Loaded converter: CONVERTER_fastq_to_fqtoc0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,113 Loaded converter: CONVERTER_gff_to_bed_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,114 Loaded converter: CONVERTER_gff_to_interval_index_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,115 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,116 Loaded converter: CONVERTER_gff_to_fli_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,117 Loaded converter: CONVERTER_gff_to_interval_index_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,119 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,120 Loaded converter: CONVERTER_interval_to_bed_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,121 Loaded converter: CONVERTER_interval_to_bedstrict_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,122 Loaded converter: CONVERTER_interval_to_bed6_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,123 Loaded converter: CONVERTER_interval_to_bed12_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,125 Loaded converter: CONVERTER_interval_to_bgzip_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,126 Loaded converter: CONVERTER_interval_to_tabix_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,127 Loaded converter: CONVERTER_interval_to_bigwig_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,128 Loaded converter: CONVERTER_picard_interval_list_to_bed6
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,129 Loaded converter: CONVERTER_maf_to_fasta_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,130 Loaded converter: CONVERTER_maf_to_interval_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,132 Loaded converter: CONVERTER_encodepeak_to_tabix_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,133 Loaded converter: CONVERTER_encodepeak_to_bgzip_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,134 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,135 Loaded converter: CONVERTER_interval_to_bgzip_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,136 Loaded converter: CONVERTER_interval_to_tabix_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,137 Loaded converter: CONVERTER_sam_to_bam
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,138 Loaded converter: CONVERTER_sam_to_bigwig_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,139 Loaded converter: tabular_to_dbnsfp
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,140 Loaded converter: CONVERTER_vcf_to_bgzip_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,141 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,142 Loaded converter: CONVERTER_vcf_to_tabix_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,144 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,145 Loaded converter: CONVERTER_wig_to_bigwig
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,146 Loaded converter: CONVERTER_wiggle_to_interval_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,147 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,148 Loaded converter: lped2fpedconvert
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,149 Loaded converter: lped2pbedconvert
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,150 Loaded converter: pbed2lpedconvert
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,151 Loaded converter: pbed2ldindepconvert
-galaxy.datatypes.registry DEBUG 2016-04-11 17:47:09,152 Loaded external metadata tool: __SET_METADATA__
-galaxy.tools.special_tools DEBUG 2016-04-11 17:47:09,154 Loaded history import tool: __IMPORT_HISTORY__
-galaxy.tools.special_tools DEBUG 2016-04-11 17:47:09,155 Loaded history export tool: __EXPORT_HISTORY__
-galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,157 VisualizationsRegistry, loaded plugin: charts
-galaxy.visualization.plugins.config_parser INFO 2016-04-11 17:47:09,158 Visualizations plugin disabled: Circster. Skipping...
-galaxy.visualization.plugins.config_parser INFO 2016-04-11 17:47:09,158 template syntax is deprecated: use entry_point instead
-galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,159 VisualizationsRegistry, loaded plugin: csg
-galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,159 VisualizationsRegistry, loaded plugin: graphview
-galaxy.visualization.plugins.config_parser INFO 2016-04-11 17:47:09,160 template syntax is deprecated: use entry_point instead
-galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,160 VisualizationsRegistry, loaded plugin: graphviz
-galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,161 VisualizationsRegistry, loaded plugin: phyloviz
-galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,162 VisualizationsRegistry, loaded plugin: scatterplot
-galaxy.visualization.plugins.config_parser INFO 2016-04-11 17:47:09,163 Visualizations plugin disabled: Sweepster. Skipping...
-galaxy.web.base.pluginframework INFO 2016-04-11 17:47:09,164 VisualizationsRegistry, loaded plugin: trackster
-galaxy.tours INFO 2016-04-11 17:47:09,198 Loaded tour 'core.history'
-galaxy.tours INFO 2016-04-11 17:47:09,244 Loaded tour 'core.galaxy_ui'
-galaxy.jobs.manager DEBUG 2016-04-11 17:47:09,248 Starting job handler
-galaxy.jobs INFO 2016-04-11 17:47:09,248 Handler 'main' will load all configured runner plugins
-galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-11 17:47:09,249 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
-galaxy.jobs.runners DEBUG 2016-04-11 17:47:09,249 Starting 5 LocalRunner workers
-galaxy.jobs DEBUG 2016-04-11 17:47:09,250 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
-galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-11 17:47:09,252 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
-galaxy.jobs.runners DEBUG 2016-04-11 17:47:09,252 Starting 2 TaskRunner workers
-galaxy.jobs DEBUG 2016-04-11 17:47:09,253 Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks'
-galaxy.jobs DEBUG 2016-04-11 17:47:09,253 Legacy destination with id 'local:///', url 'local:///' converted, got params:
-galaxy.jobs.handler DEBUG 2016-04-11 17:47:09,253 Loaded job runners plugins: tasks:local
-galaxy.jobs.handler INFO 2016-04-11 17:47:09,253 job handler stop queue started
-galaxy.jobs.handler INFO 2016-04-11 17:47:09,272 job handler queue started
-galaxy.sample_tracking.external_service_types DEBUG 2016-04-11 17:47:09,280 Loaded external_service_type: Simple unknown sequencer 1.0.0
-galaxy.sample_tracking.external_service_types DEBUG 2016-04-11 17:47:09,282 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
-galaxy.workflow.scheduling_manager DEBUG 2016-04-11 17:47:09,285 Starting workflow schedulers
-functional_tests.py INFO 2016-04-11 17:47:09,287 Embedded Universe application started
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,299 Enabling 'search' controller, class: SearchController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,302 Enabling 'library_common' controller, class: LibraryCommon
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,303 Enabling 'userskeys' controller, class: User
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,305 Enabling 'request_type' controller, class: RequestType
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,306 Enabling 'tag' controller, class: TagsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,311 Enabling 'workflow' controller, class: WorkflowController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,311 Enabling 'data_manager' controller, class: DataManager
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,312 Enabling 'requests_admin' controller, class: RequestsAdmin
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,314 Enabling 'requests_common' controller, class: RequestsCommon
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,314 Enabling 'requests' controller, class: Requests
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,317 Enabling 'forms' controller, class: Forms
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,387 Enabling 'admin_toolshed' controller, class: AdminGalaxy
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,387 Enabling 'admin_toolshed' controller, class: AdminToolshed
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,388 Enabling 'root' controller, class: RootController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,389 Enabling 'admin' controller, class: AdminGalaxy
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,390 Enabling 'history' controller, class: HistoryController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,392 Enabling 'user' controller, class: User
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,392 Enabling 'library' controller, class: Library
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,393 Enabling 'biostar' controller, class: BiostarController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,393 Enabling 'external_services' controller, class: ExternalServiceController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,393 Enabling 'external_service' controller, class: ExternalService
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,395 Enabling 'visualization' controller, class: VisualizationController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,395 Enabling 'async' controller, class: ASync
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,396 Enabling 'library_admin' controller, class: LibraryAdmin
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,396 Enabling 'dataset' controller, class: DatasetInterface
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,397 Enabling 'mobile' controller, class: Mobile
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,398 Enabling 'page' controller, class: PageController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,398 Enabling 'error' controller, class: Error
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,399 Enabling 'tool_runner' controller, class: ToolRunner
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,419 Enabling 'search' API controller, class: SearchController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,420 Enabling 'libraries' API controller, class: LibrariesController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,420 Enabling 'group_roles' API controller, class: GroupRolesAPIController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,420 Enabling 'authenticate' API controller, class: AuthenticationController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,421 Enabling 'users' API controller, class: UserAPIController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,421 Enabling 'roles' API controller, class: RoleAPIController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,422 Enabling 'groups' API controller, class: GroupAPIController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,422 Enabling 'metrics' API controller, class: MetricsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,422 Enabling 'datatypes' API controller, class: DatatypesController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,423 Enabling 'history_contents' API controller, class: HistoryContentsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,423 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,424 Enabling 'tools' API controller, class: ToolsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,424 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,425 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,425 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,425 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,426 Enabling 'quotas' API controller, class: QuotaAPIController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,426 Enabling 'requests' API controller, class: RequestsAPIController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,426 Enabling 'page_revisions' API controller, class: PageRevisionsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,427 Enabling 'forms' API controller, class: FormDefinitionAPIController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,427 Enabling 'samples' API controller, class: SamplesAPIController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,427 Enabling 'pages' API controller, class: PagesController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,428 Enabling 'configuration' API controller, class: ConfigurationController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,428 Enabling 'tours' API controller, class: ToursController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,428 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,428 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,429 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,429 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,429 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,429 Enabling 'tool_data' API controller, class: ToolData
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,430 Enabling 'genomes' API controller, class: GenomesController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,430 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,431 Enabling 'folders' API controller, class: FoldersController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,431 Enabling 'library_contents' API controller, class: LibraryContentsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,432 Enabling 'workflows' API controller, class: WorkflowsAPIController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,432 Enabling 'visualizations' API controller, class: VisualizationsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,433 Enabling 'datasets' API controller, class: DatasetsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,433 Enabling 'histories' API controller, class: HistoriesController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,434 Enabling 'group_users' API controller, class: GroupUsersAPIController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,434 Enabling 'jobs' API controller, class: JobController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,435 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,435 Enabling 'history_tags' API controller, class: HistoryTagsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,435 Enabling 'workflow_tags' API controller, class: WorkflowTagsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,435 Enabling 'request_types' API controller, class: RequestTypeAPIController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,436 Enabling 'remote_files' API controller, class: RemoteFilesAPIController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,437 Enabling 'folder_contents' API controller, class: FolderContentsController
-galaxy.web.framework.base DEBUG 2016-04-11 17:47:09,437 Enabling 'job_files' API controller, class: JobFilesAPIController
-galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,915 Enabling 'httpexceptions' middleware
-galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,916 Enabling 'recursive' middleware
-galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,926 Enabling 'error' middleware
-galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,926 Enabling 'x-forwarded-host' middleware
-galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,926 Enabling 'Request ID' middleware
-galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,932 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static
-galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,932 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static
-galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,932 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static
-galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,933 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static
-galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 17:47:09,933 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static
-galaxy.queue_worker INFO 2016-04-11 17:47:09,933 Binding and starting galaxy control worker for main
-functional_tests.py DEBUG 2016-04-11 17:47:09,933 Attempting to serve app on randomly chosen port: 9522
-functional_tests.py INFO 2016-04-11 17:47:10,069 Embedded web server started
-functional_tests.py INFO 2016-04-11 17:47:10,070 Functional tests will be run against localhost:9522
-galaxy.tools.toolbox.watcher INFO 2016-04-11 17:47:10,071 Watchdog library unavailble, cannot monitor tools.
-galaxy.tools.toolbox.base INFO 2016-04-11 17:47:10,071 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/tool_conf.xml
-galaxy.tools.toolbox.base INFO 2016-04-11 17:47:10,071 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/config/shed_tool_conf.xml
-galaxy.tools.toolbox.base INFO 2016-04-11 17:47:10,097 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/empty_tool_conf.xml
-galaxy.tools.toolbox.base INFO 2016-04-11 17:47:10,097 Parsing the tool configuration /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/config/shed_tool_conf.xml
-galaxy.tools.toolbox.base DEBUG 2016-04-11 17:47:10,175 Loaded tool id: upload1, version: 1.1.4 into tool panel..
-galaxy.tools.toolbox.base DEBUG 2016-04-11 17:47:10,175 Loading section: Shed Installs
-galaxy.tools.toolbox.base DEBUG 2016-04-11 17:47:10,400 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 2016-04-11 17:47:10,401 Unable to find config file './dependency_resolvers_conf.xml'
-[?1034hbase.asserts DEBUG 2016-04-11 17:47:10,504 base.asserts.text
-base.asserts DEBUG 2016-04-11 17:47:10,505 base.asserts.tabular
-base.asserts DEBUG 2016-04-11 17:47:10,505 base.asserts.xml
-nose.plugins.manager DEBUG 2016-04-11 17:47:10,516 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:10,589 Starting new HTTP connection (1): localhost
-galaxy.web.framework.webapp INFO 2016-04-11 17:47:10,593 Session authenticated using Galaxy master api key
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:10,604 "GET /api/users?key=test_key HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:10,628 Starting new HTTP connection (1): localhost
-galaxy.web.framework.webapp INFO 2016-04-11 17:47:10,631 Session authenticated using Galaxy master api key
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:11,136 "POST /api/users HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:11,138 Starting new HTTP connection (1): localhost
-galaxy.web.framework.webapp INFO 2016-04-11 17:47:11,144 Session authenticated using Galaxy master api key
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:11,236 "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:11,238 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:11,438 "POST /api/histories HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:11,455 Starting new HTTP connection (1): localhost
-galaxy.tools DEBUG 2016-04-11 17:47:11,695 Validated and populated state for tool request (18.524 ms)
-galaxy.tools.actions.upload DEBUG 2016-04-11 17:47:11,739 Persisted uploads (20.819 ms)
-galaxy.tools.actions.upload DEBUG 2016-04-11 17:47:12,160 Checked and cleaned uploads (421.017 ms)
-galaxy.tools.actions.upload_common INFO 2016-04-11 17:47:12,256 tool upload1 created job id 1
-galaxy.tools.actions.upload DEBUG 2016-04-11 17:47:12,372 Created upload job (212.151 ms)
-galaxy.tools.execute DEBUG 2016-04-11 17:47:12,373 Tool [upload1] created job [1] (654.615 ms)
-galaxy.tools.execute DEBUG 2016-04-11 17:47:12,395 Executed all jobs for tool request: (699.689 ms)
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:12,462 "POST /api/tools HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:12,464 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:12,548 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:12,550 Starting new HTTP connection (1): localhost
-galaxy.jobs DEBUG 2016-04-11 17:47:12,600 (1) Working directory for job is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1
-galaxy.jobs.handler DEBUG 2016-04-11 17:47:12,633 (1) Dispatching to local runner
-galaxy.jobs DEBUG 2016-04-11 17:47:12,712 (1) Persisting job destination (destination id: local:///)
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:12,734 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:12,736 Starting new HTTP connection (1): localhost
-galaxy.jobs.runners DEBUG 2016-04-11 17:47:12,778 Job [1] queued (144.152 ms)
-galaxy.jobs.handler INFO 2016-04-11 17:47:12,818 (1) Job dispatched
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:12,973 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:12,975 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:13,225 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:13,227 Starting new HTTP connection (1): localhost
-galaxy.tools.deps DEBUG 2016-04-11 17:47:13,428 Building dependency shell command for dependency 'samtools'
-galaxy.tools.deps DEBUG 2016-04-11 17:47:13,428 Find dependency samtools version None
-galaxy.tools.deps DEBUG 2016-04-11 17:47:13,428 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:13,428 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:13,428 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:13,429 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:13,429 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps WARNING 2016-04-11 17:47:13,429 Failed to resolve dependency on 'samtools', ignoring
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:13,450 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:13,452 Starting new HTTP connection (1): localhost
-galaxy.jobs.command_factory INFO 2016-04-11 17:47:13,520 Built script [/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev/tools/data_source/upload.py /tmp/713417.1.short.q/tmp32I4oD/galaxy-dev /tmp/713417.1.short.q/tmp32I4oD/tmp/tmpIuu2Wr /tmp/713417.1.short.q/tmp32I4oD/tmp/tmpKio67E 1:/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/dataset_1_files:/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_1.dat]
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:13,704 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:13,707 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:13,918 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:13,920 Starting new HTTP connection (1): localhost
-galaxy.jobs.runners DEBUG 2016-04-11 17:47:13,959 (1) command is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/set_metadata_aCYbsb.py" "/tmp/713417.1.short.q/tmp32I4oD/tmp/tmpIuu2Wr" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/galaxy.json" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_XozciK,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_PCVo6A,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_POL2Ze,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_3vJ9WJ,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_1.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_hQCXbL" 5242880; sh -c "exit $return_code"
-galaxy.jobs.runners.local DEBUG 2016-04-11 17:47:13,974 (1) executing job script: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/galaxy_1.sh
-galaxy.jobs DEBUG 2016-04-11 17:47:13,987 (1) Persisting job destination (destination id: local:///)
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:14,106 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:17,054 Starting new HTTP connection (1): localhost
-galaxy.jobs.runners.local DEBUG 2016-04-11 17:47:17,054 execution finished: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/1/galaxy_1.sh
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:17,291 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:17,294 Starting new HTTP connection (1): localhost
-galaxy.datatypes.metadata DEBUG 2016-04-11 17:47:17,353 loading metadata from file for: HistoryDatasetAssociation 1
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:17,477 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:17,479 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:17,677 "GET /api/histories/2891970512fa2d5a?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:17,679 Starting new HTTP connection (1): localhost
-galaxy.tools DEBUG 2016-04-11 17:47:17,859 Validated and populated state for tool request (99.599 ms)
-galaxy.jobs DEBUG 2016-04-11 17:47:17,919 job 1 ended (finish() executed in (864.203 ms))
-galaxy.tools.actions INFO 2016-04-11 17:47:18,029 Handled output (134.928 ms)
-galaxy.tools.actions INFO 2016-04-11 17:47:18,101 Handled output (71.983 ms)
-galaxy.tools.actions INFO 2016-04-11 17:47:18,192 Handled output (90.651 ms)
-galaxy.tools.actions INFO 2016-04-11 17:47:18,283 Handled output (90.794 ms)
-galaxy.tools.actions INFO 2016-04-11 17:47:18,383 Verified access to datasets (8.282 ms)
-galaxy.tools.execute DEBUG 2016-04-11 17:47:18,487 Tool [testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] created job [2] (601.149 ms)
-galaxy.tools.execute DEBUG 2016-04-11 17:47:18,505 Executed all jobs for tool request: (646.356 ms)
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:18,635 "POST /api/tools HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:18,637 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:18,965 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-galaxy.jobs DEBUG 2016-04-11 17:47:19,038 (2) Working directory for job is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2
-galaxy.jobs.handler DEBUG 2016-04-11 17:47:19,056 (2) Dispatching to local runner
-galaxy.jobs DEBUG 2016-04-11 17:47:19,105 (2) Persisting job destination (destination id: local:///)
-galaxy.jobs.runners DEBUG 2016-04-11 17:47:19,162 Job [2] queued (106.028 ms)
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:19,189 Starting new HTTP connection (1): localhost
-galaxy.jobs.handler INFO 2016-04-11 17:47:19,255 (2) Job dispatched
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:19,562 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,849 Building dependency shell command for dependency 'R'
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,849 Find dependency R version 3.1.2
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,858 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2ac7e450d110> (isnull? False)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,858 Building dependency shell command for dependency 'r-snow'
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,858 Find dependency r-snow version 0.4_1
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,858 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps WARNING 2016-04-11 17:47:19,859 Failed to resolve dependency on 'r-snow', ignoring
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Building dependency shell command for dependency 'bioconductor-camera'
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Find dependency bioconductor-camera version 1.44.0
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,859 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps WARNING 2016-04-11 17:47:19,860 Failed to resolve dependency on 'bioconductor-camera', ignoring
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Building dependency shell command for dependency 'r-batch'
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Find dependency r-batch version 1.1_4
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3d78090> (isnull? True)
-galaxy.tools.deps WARNING 2016-04-11 17:47:19,860 Failed to resolve dependency on 'r-batch', ignoring
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,860 Building dependency shell command for dependency 'graphicsmagick'
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,861 Find dependency graphicsmagick version 1.3.20
-galaxy.tools.deps DEBUG 2016-04-11 17:47:19,861 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2ac83c0d9a50> (isnull? False)
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:19,965 Starting new HTTP connection (1): localhost
-galaxy.jobs.command_factory INFO 2016-04-11 17:47:19,988 Built script [/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/713417.1.short.q/tmp32I4oD/deps/R/3.1.2/lecorguille/camera_annotate/c02d80efba80; export PACKAGE_BASE; . /tmp/713417.1.short.q/tmp32I4oD/deps/R/3.1.2/lecorguille/camera_annotate/c02d80efba80/env.sh; PACKAGE_BASE=/tmp/713417.1.short.q/tmp32I4oD/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/c02d80efba80; export PACKAGE_BASE; . /tmp/713417.1.short.q/tmp32I4oD/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/c02d80efba80/env.sh; LANG=C Rscript /tmp/713417.1.short.q/tmp32I4oD/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/c02d80efba80/camera_annotate/CAMERA.r  xfunction annotatediff image /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_1.dat  variableMetadataOutput /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_2.dat dataMatrixOutput /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_3.dat xsetRdataOutput /tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_4.dat  convert_param FALSE num_digits 0 nSlaves ${GALAXY_SLOTS:-1} sigma 6 perfwhm 0.6 maxcharge 3 maxiso 4 minfrac 0.5 ppm 5 mzabs 0.015 intval into max_peaks 100 quick FALSE polarity negative cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE multiplier 3  runDiffreport TRUE eicmax 200 eicwidth 200 value into sortpval FALSE h 480 w 640 mzdec 2 new_file_path /tmp/713417.1.short.q/tmp32I4oD/tmp/primary_5_]
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:20,213 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-galaxy.jobs.runners DEBUG 2016-04-11 17:47:20,976 (2) command is: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/tool_script.sh; return_code=$?; python "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/set_metadata_7oSiGt.py" "/tmp/713417.1.short.q/tmp32I4oD/tmp/tmpIuu2Wr" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/galaxy.json" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_yQypOr,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_5pYigd,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_dqnE6s,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_bb9G1l,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_2.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_qGNTro" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_3_GFPZBf,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_3_dzMzqz,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_3_YTXBdt,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_3_60vr5_,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_3.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_3_CF9v7P" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_4_dtyp5t,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_4_0jY9lR,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_4_IYAPP7,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_4_g18Jla,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_4.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_4_YPXaBQ" "/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_5_w61b96,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_5_oh73F9,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_5_jXk9Pn,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_5_GgatPH,/tmp/713417.1.short.q/tmp32I4oD/files/000/dataset_5.dat,/tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_5_lY8WCQ" 5242880; sh -c "exit $return_code"
-galaxy.jobs.runners.local DEBUG 2016-04-11 17:47:20,990 (2) executing job script: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/galaxy_2.sh
-galaxy.jobs DEBUG 2016-04-11 17:47:20,997 (2) Persisting job destination (destination id: local:///)
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:21,018 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:21,415 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:23,019 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:23,187 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-galaxy.jobs.runners.local DEBUG 2016-04-11 17:47:23,589 execution finished: /tmp/713417.1.short.q/tmp32I4oD/job_working_directory/000/2/galaxy_2.sh
-galaxy.jobs.output_checker INFO 2016-04-11 17:47:23,636 Job 2: Fatal error: Exit code 1 ()
-galaxy.jobs.output_checker DEBUG 2016-04-11 17:47:23,636 Tool exit code indicates an error, failing job.
-galaxy.jobs DEBUG 2016-04-11 17:47:23,731 (2) setting dataset 2 state to ERROR
-galaxy.jobs DEBUG 2016-04-11 17:47:23,773 (2) setting dataset 3 state to ERROR
-galaxy.jobs DEBUG 2016-04-11 17:47:23,814 (2) setting dataset 4 state to ERROR
-galaxy.jobs DEBUG 2016-04-11 17:47:23,858 (2) setting dataset 5 state to ERROR
-galaxy.jobs DEBUG 2016-04-11 17:47:24,240 job 2 ended (finish() executed in (651.127 ms))
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:26,393 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:26,590 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:26,592 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:26,649 "GET /api/histories/2891970512fa2d5a/contents?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:26,651 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:26,844 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:26,846 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:26,971 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:26,973 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:27,152 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:27,154 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:27,284 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:27,286 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:27,462 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:27,464 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:27,642 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:27,644 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:28,025 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:28,027 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:28,150 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:28,152 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:28,325 "GET /api/jobs/5729865256bc2525?full=true&key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:28,327 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:28,485 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:28,487 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:28,544 "GET /api/histories/2891970512fa2d5a/contents?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:28,546 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:28,769 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:28,771 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:28,893 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:28,895 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:29,087 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:29,089 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:29,213 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:29,215 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:29,395 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:29,397 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:29,520 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:29,522 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:29,733 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:29,735 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:29,863 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:29,865 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:30,034 "GET /api/jobs/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:30,036 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:30,095 "GET /api/histories/2891970512fa2d5a/contents?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
-requests.packages.urllib3.connectionpool INFO 2016-04-11 17:47:30,097 Starting new HTTP connection (1): localhost
-requests.packages.urllib3.connectionpool DEBUG 2016-04-11 17:47:30,280 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=f72741b00e6cec9e3d02042b5508bb4d HTTP/1.1" 200 None
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+migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py...
+migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully
+migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py...
+migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully
+migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py...
+migrate.versioning.script.base DEBUG 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
 testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3[0]: failed
-testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3[0]: failed
Binary file test-data/xset.group.retcor.group.fillPeaks.RData has changed