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test egsea 1.20.0 #76

Closed
jennaj opened this issue Feb 15, 2023 · 2 comments
Closed

test egsea 1.20.0 #76

jennaj opened this issue Feb 15, 2023 · 2 comments

Comments

@jennaj
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Collaborator

jennaj commented Feb 15, 2023

toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0

user reported in bugs -- most outputs selected -- and at least one is missing a dependency (?). Seems new.

stderr
Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
OS reports request to set locale to "en_US.UTF-8" cannot be honored

groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Error: package or namespace load failed for 'EGSEA':
.onLoad failed in loadNamespace() for 'HDF5Array', details:
call: H5Fcreate(file)
error: HDF5. File accessibility. Unable to open file.
@jennaj
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Collaborator Author

jennaj commented Feb 15, 2023

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.20.0

@mvdbeek
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mvdbeek commented Feb 15, 2023

Results (powered by Planemo)

Summary

State Count
Total 7
Passed 7
Error 0
Failure 0
Skipped 0
Passed s
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea (Test tool test #1)

    Command Line:

    • 

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
EGSEA analysis has started
Log fold changes are estimated using limma package ... 
limma DE analysis is carried out ... 
EGSEA is running on the provided data and h collection
..globaltest*camera*.ora*
EGSEA analysis took 7.691 seconds.
EGSEA analysis has completed
EGSEA HTML report is being generated ...
Report pages and figures are being generated for the h collection ...
   Heat maps are being generated for top-ranked gene sets 
based on logFC ... 
   Summary plots are being generated ... 
EGSEA report generation took 17.538 seconds.
EGSEA report has been generated.

      

      • 

    

    Standard Output:
    

      

    • 

      [1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Feb 14 18:18:26 2023 ------##
##------ Tue Feb 14 18:18:34 2023 ------##
##------ Tue Feb 14 18:18:34 2023 ------##
##------ Tue Feb 14 18:18:51 2023 ------##

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
input
{"__current_case__": 1, "counts": {"values": [{"id": 108312158, "src": "hda"}]}, "fact": {"__current_case__": 1, "ffile": "no", "rep_factor": [{"__index__": 0, "factorName": "Treatment", "groupNames": "IL13,IL13Ant,IL13,IL13,IL13Ant"}]}, "format": "matrix"}

      

      
rep_contrast
[{"__index__": 0, "contrast": "IL13Ant-IL13"}]

      

      
species
"human"

      

      
base_methods
["camera", "globaltest", "ora"]

      

      
msigdb
{"msigdb_gsets": "h"}

      

      
keggdb
{"kegg_updated": false, "keggdb_gsets": null}

      

      
gsdb
{"gsdb_gsets": null}

      

      
advanced
{"combine_method": "wilkinson", "display_top": "5", "fdr_cutoff": "0.05", "min_size": "2", "rdaOpt": false, "rscriptOpt": false, "sort_method": "med.rank"}

      

      
non_commercial_use
true

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"auto"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea (Test test against test.galaxyproject.org #2)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
EGSEA analysis has started
Log fold changes are estimated using limma package ... 
limma DE analysis is carried out ... 
EGSEA is running on the provided data and h collection
..globaltest*camera*.ora*
EGSEA analysis took 11.809 seconds.
EGSEA analysis has completed
EGSEA HTML report is being generated ...
Report pages and figures are being generated for the h collection ...
   Heat maps are being generated for top-ranked gene sets 
based on logFC ... 
   Summary plots are being generated ... 
EGSEA report generation took 72.774 seconds.
EGSEA report has been generated.

      

      • 

    

    Standard Output:
    

      

    • 

      [1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Feb 14 18:24:29 2023 ------##
##------ Tue Feb 14 18:24:40 2023 ------##
##------ Tue Feb 14 18:24:41 2023 ------##
##------ Tue Feb 14 18:25:54 2023 ------##

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
input
{"__current_case__": 1, "counts": {"values": [{"id": 108312158, "src": "hda"}]}, "fact": {"__current_case__": 0, "ffile": "yes", "finfo": {"values": [{"id": 108312163, "src": "hda"}]}}, "format": "matrix"}

      

      
rep_contrast
[{"__index__": 0, "contrast": "IL13Ant-IL13"}]

      

      
species
"human"

      

      
base_methods
["camera", "globaltest", "ora"]

      

      
msigdb
{"msigdb_gsets": "h"}

      

      
keggdb
{"kegg_updated": false, "keggdb_gsets": null}

      

      
gsdb
{"gsdb_gsets": null}

      

      
advanced
{"combine_method": "wilkinson", "display_top": "5", "fdr_cutoff": "0.05", "min_size": "2", "rdaOpt": false, "rscriptOpt": true, "sort_method": "med.rank"}

      

      
non_commercial_use
true

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"tabular"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea (Test Test Prokka 1.14.6+galaxy1 #3)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
EGSEA analysis has started
Log fold changes are estimated using limma package ... 
limma DE analysis is carried out ... 
EGSEA is running on the provided data and h collection
....camera*globaltest*..ora*
EGSEA analysis took 26.103 seconds.
EGSEA analysis has completed
EGSEA HTML report is being generated ...
Report pages and figures are being generated for the h collection ...
   Heat maps are being generated for top-ranked gene sets 
based on logFC ... 
   Summary plots are being generated ... 
   Comparison summary plots are being generated  ...
EGSEA report generation took 224.219 seconds.
EGSEA report has been generated.

      

      • 

    

    Standard Output:
    

      

    • 

      [1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Feb 14 18:29:46 2023 ------##
##------ Tue Feb 14 18:30:13 2023 ------##
##------ Tue Feb 14 18:30:13 2023 ------##
##------ Tue Feb 14 18:33:57 2023 ------##

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
input
{"__current_case__": 1, "counts": {"values": [{"id": 108312158, "src": "hda"}]}, "fact": {"__current_case__": 0, "ffile": "yes", "finfo": {"values": [{"id": 108312163, "src": "hda"}]}}, "format": "matrix"}

      

      
rep_contrast
[{"__index__": 0, "contrast": "IL13Ant-IL13"}, {"__index__": 1, "contrast": "IL13-IL13Ant"}]

      

      
species
"human"

      

      
base_methods
["camera", "globaltest", "ora"]

      

      
msigdb
{"msigdb_gsets": "h"}

      

      
keggdb
{"kegg_updated": false, "keggdb_gsets": null}

      

      
gsdb
{"gsdb_gsets": null}

      

      
advanced
{"combine_method": "wilkinson", "display_top": "5", "fdr_cutoff": "0.05", "min_size": "2", "rdaOpt": false, "rscriptOpt": false, "sort_method": "med.rank"}

      

      
non_commercial_use
true

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"tabular"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea (Test Test roary 3.13.0+galaxy2 #4)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
EGSEA analysis has started
Log fold changes are estimated using limma package ... 
limma DE analysis is carried out ... 
EGSEA is running on the provided data and h collection
..globaltest*camera*.ora*
EGSEA analysis took 8.328 seconds.
EGSEA analysis has completed
EGSEA HTML report is being generated ...
Report pages and figures are being generated for the h collection ...
   Heat maps are being generated for top-ranked gene sets 
based on logFC ... 
   Summary plots are being generated ... 
EGSEA report generation took 16.452 seconds.
EGSEA report has been generated.

      

      • 

    

    Standard Output:
    

      

    • 

      [1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Feb 14 18:19:15 2023 ------##
##------ Tue Feb 14 18:19:23 2023 ------##
##------ Tue Feb 14 18:19:23 2023 ------##
##------ Tue Feb 14 18:19:40 2023 ------##

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
input
{"__current_case__": 1, "counts": {"values": [{"id": 108312158, "src": "hda"}]}, "fact": {"__current_case__": 0, "ffile": "yes", "finfo": {"values": [{"id": 108312164, "src": "hda"}]}}, "format": "matrix"}

      

      
rep_contrast
[{"__index__": 0, "contrast": "IL13Ant-IL13"}]

      

      
species
"human"

      

      
base_methods
["camera", "globaltest", "ora"]

      

      
msigdb
{"msigdb_gsets": "h"}

      

      
keggdb
{"kegg_updated": false, "keggdb_gsets": null}

      

      
gsdb
{"gsdb_gsets": null}

      

      
advanced
{"combine_method": "wilkinson", "display_top": "5", "fdr_cutoff": "0.05", "min_size": "2", "rdaOpt": false, "rscriptOpt": false, "sort_method": "med.rank"}

      

      
non_commercial_use
true

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"tabular"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
EGSEA analysis has started
Log fold changes are estimated using limma package ... 
limma DE analysis is carried out ... 
EGSEA is running on the provided data and h collection
......gage*.safe*globaltest*...zscore*.camera*.ssgsea*roast*.gsva*..fry*ora*.plage*padog*
EGSEA analysis took 25.536 seconds.
EGSEA analysis has completed
EGSEA HTML report is being generated ...
Report pages and figures are being generated for the h collection ...
   Heat maps are being generated for top-ranked gene sets 
based on logFC ... 
   Summary plots are being generated ... 
EGSEA report generation took 80.473 seconds.
EGSEA report has been generated.

      

      • 

    

    Standard Output:
    

      

    • 

      [1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Feb 14 18:20:46 2023 ------##
##------ Tue Feb 14 18:21:12 2023 ------##
##------ Tue Feb 14 18:21:13 2023 ------##
##------ Tue Feb 14 18:22:33 2023 ------##

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
input
{"__current_case__": 1, "counts": {"values": [{"id": 108312158, "src": "hda"}]}, "fact": {"__current_case__": 0, "ffile": "yes", "finfo": {"values": [{"id": 108312164, "src": "hda"}]}}, "format": "matrix"}

      

      
rep_contrast
[{"__index__": 0, "contrast": "IL13Ant-IL13"}]

      

      
species
"human"

      

      
base_methods
["camera", "safe", "gage", "zscore", "gsva", "globaltest", "ora", "ssgsea", "padog", "plage", "fry", "roast"]

      

      
msigdb
{"msigdb_gsets": "h"}

      

      
keggdb
{"kegg_updated": false, "keggdb_gsets": null}

      

      
gsdb
{"gsdb_gsets": null}

      

      
advanced
{"combine_method": "wilkinson", "display_top": "5", "fdr_cutoff": "0.05", "min_size": "2", "rdaOpt": false, "rscriptOpt": false, "sort_method": "med.rank"}

      

      
non_commercial_use
true

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"tabular"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea (Test Test trinotate 3.2.2+galaxy0 #6)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
EGSEA analysis has started
Log fold changes are estimated using limma package ... 
limma DE analysis is carried out ... 
EGSEA is running on the provided data and h collection
..globaltest*camera*.ora*
EGSEA is running on the provided data and kegg collection
..globaltest*camera*.ora*
EGSEA analysis took 13.279 seconds.
EGSEA analysis has completed
EGSEA HTML report is being generated ...
Report pages and figures are being generated for the h collection ...
   Heat maps are being generated for top-ranked gene sets 
based on logFC ... 
   Summary plots are being generated ... 
Report pages and figures are being generated for the kegg collection ...
   Pathway maps are being generated for top-ranked 
 pathways based on logFC ... 
   Heat maps are being generated for top-ranked gene sets 
based on logFC ... 
   Summary plots are being generated ... 
EGSEA report generation took 125.054 seconds.
EGSEA report has been generated.

      

      • 

    

    Standard Output:
    

      

    • 

      [1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
[1] "Building KEGG pathways annotation object ... "
##------ Tue Feb 14 18:28:14 2023 ------##
##------ Tue Feb 14 18:28:27 2023 ------##
##------ Tue Feb 14 18:28:27 2023 ------##
##------ Tue Feb 14 18:30:32 2023 ------##

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
input
{"__current_case__": 1, "counts": {"values": [{"id": 108312158, "src": "hda"}]}, "fact": {"__current_case__": 0, "ffile": "yes", "finfo": {"values": [{"id": 108312164, "src": "hda"}]}}, "format": "matrix"}

      

      
rep_contrast
[{"__index__": 0, "contrast": "IL13Ant-IL13"}]

      

      
species
"human"

      

      
base_methods
["camera", "globaltest", "ora"]

      

      
msigdb
{"msigdb_gsets": "h"}

      

      
keggdb
{"kegg_updated": true, "keggdb_gsets": "keggmet"}

      

      
gsdb
{"gsdb_gsets": null}

      

      
advanced
{"combine_method": "wilkinson", "display_top": "5", "fdr_cutoff": "0.05", "min_size": "2", "rdaOpt": false, "rscriptOpt": false, "sort_method": "med.rank"}

      

      
non_commercial_use
true

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"tabular"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea (Test Test pangolin 3.1.17+galaxy1 #7)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
EGSEA analysis has started
Log fold changes are estimated using limma package ... 
limma DE analysis is carried out ... 
EGSEA is running on the provided data and h collection
..globaltest*camera*.ora*
EGSEA analysis took 9.145 seconds.
EGSEA analysis has completed
EGSEA HTML report is being generated ...
Report pages and figures are being generated for the h collection ...
   Heat maps are being generated for top-ranked gene sets 
based on logFC ... 
   Summary plots are being generated ... 
EGSEA report generation took 15.473 seconds.
EGSEA report has been generated.

      

      • 

    

    Standard Output:
    

      

    • 

      [1] "Loading MSigDB Gene Sets ... "
[1] "Loaded gene sets for the collection h ..."
[1] "Indexed the collection h ..."
[1] "Created annotation for the collection h ..."
##------ Tue Feb 14 18:22:25 2023 ------##
##------ Tue Feb 14 18:22:34 2023 ------##
##------ Tue Feb 14 18:22:34 2023 ------##
##------ Tue Feb 14 18:22:50 2023 ------##

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
input
{"__current_case__": 0, "format": "files", "rep_factor": [{"__index__": 0, "factorName": "Treatment", "rep_group": [{"__index__": 0, "countsFile": {"values": [{"id": 108312174, "src": "hda"}, {"id": 108312176, "src": "hda"}, {"id": 108312177, "src": "hda"}]}, "groupName": "IL13"}, {"__index__": 1, "countsFile": {"values": [{"id": 108312175, "src": "hda"}, {"id": 108312178, "src": "hda"}]}, "groupName": "IL13Ant"}]}, {"__index__": 1, "factorName": "Batch", "rep_group": [{"__index__": 0, "countsFile": {"values": [{"id": 108312174, "src": "hda"}, {"id": 108312175, "src": "hda"}]}, "groupName": "b1"}, {"__index__": 1, "countsFile": {"values": [{"id": 108312176, "src": "hda"}, {"id": 108312177, "src": "hda"}, {"id": 108312178, "src": "hda"}]}, "groupName": "b2"}]}]}

      

      
rep_contrast
[{"__index__": 0, "contrast": "IL13Ant-IL13"}]

      

      
species
"human"

      

      
base_methods
["camera", "globaltest", "ora"]

      

      
msigdb
{"msigdb_gsets": "h"}

      

      
keggdb
{"kegg_updated": false, "keggdb_gsets": null}

      

      
gsdb
{"gsdb_gsets": null}

      

      
advanced
{"combine_method": "wilkinson", "display_top": "5", "fdr_cutoff": "0.05", "min_size": "2", "rdaOpt": false, "rscriptOpt": false, "sort_method": "med.rank"}

      

      
non_commercial_use
true

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"tabular"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
            

    

      
    

    


      

          @jennaj
jennaj




            closed this as completed


      Feb 22, 2023

    

  


    











  
  

    

      

  





  




  
  

              

  
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      2 participants
    

    

        
          @mvdbeek 
        
          @jennaj