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Test trinotate 3.2.2+galaxy0 #6

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natefoo opened this issue Dec 7, 2021 · 5 comments
Closed

Test trinotate 3.2.2+galaxy0 #6

natefoo opened this issue Dec 7, 2021 · 5 comments

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@natefoo
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natefoo commented Dec 7, 2021

Installed in galaxyproject/usegalaxy-tools#448
@natefoo
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natefoo commented Dec 7, 2021

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.2.2+galaxy0

@mvdbeek
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mvdbeek commented Dec 7, 2021

Results (powered by Planemo)

Summary

State Count
Total 2
Passed 0
Error 1
Failure 1
Skipped 0
Errored s
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate (Test test against test.galaxyproject.org #2)

    Execution Problem:

    • Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .
Failed s
  • ❌ toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate (Test tool test #1)

    Problems:

    • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.2.2+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/039/504/39504519/tool_script.sh: line 9: Build_Trinotate_Boilerplate_SQLite_db.pl: not found
.

    • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.2.2+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/039/504/39504519/tool_script.sh: line 9: Build_Trinotate_Boilerplate_SQLite_db.pl: not found
.

    Command Line:

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      • 

    

    Exit Code:
    

      

    • 

      127
      

      • 

    

    Standard Error:
    

      

    • 

      /corral4/main/jobs/039/504/39504519/tool_script.sh: line 9: Build_Trinotate_Boilerplate_SQLite_db.pl: not found

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
cond_download
{"__current_case__": 1, "select_download": "yes"}

      

      
report_option
{"E": "1e-05", "incl_pep": "false", "incl_trans": "false", "pfam_cutoff": "DNC"}

      

      
keep_sqlite
"false"

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

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  @natefoo





  


    

      

  

    

        
    
    

  


      
          
  
      
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    Collaborator


      

  Author


  


  

    

      

      
            natefoo
  

      

      

      commented


        Dec 21, 2021


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.2.2+galaxy0


Might fail due to output size differences but the tool should run now. Here's what I got locally:


Expected file size was 573911, actual file size was 573236 (difference of 100 accepted)


      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
            Copy link

  

      
    

  


  

      

  
    Owner


      

  


  

    

      

      
            mvdbeek
  

      

      

      commented


        Dec 21, 2021


      
    


  





      


        


  
    

      
          
Results (powered by Planemo)


Summary



  

  

  

  

  

  








State
Count






Total
2




Passed
0




Error
0




Failure
2




Skipped
0






Failed s

    

  • 

    ❌ toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate (Test tool test #1)
    

    Problems:
    

      

    • 

      Output trinotate_out:  different than expected, difference (using diff):
( /tmp/tmpv_iw52ritrinotate_annotation_report.xls v. /tmp/tmp587viv5wtrinotate_annotation_report.xls )
--- local_file
+++ history_data
@@ -6,9 +6,9 @@
 TRINITY_DN594_c0_g2	TRINITY_DN594_c0_g2_i1	ERG27_SCHPO^ERG27_SCHPO^Q:1207-680,H:46-205^90.91%ID^E:2e-141^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces`ERG27_SCHPO^ERG27_SCHPO^Q:681-349,H:228-338^100%ID^E:2e-141^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	TRINITY_DN594_c0_g2_i1|m.613	653-1207[-]	ERG27_SCHPO^ERG27_SCHPO^Q:1-176,H:46-205^90.91%ID^E:2e-108^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	.	.	.	KEGG:spo:SPBC1709.07	GO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0005811^cellular_component^lipid droplet`GO:0000253^molecular_function^3-keto sterol reductase activity`GO:0006696^biological_process^ergosterol biosynthetic process	GO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0005811^cellular_component^lipid droplet`GO:0000253^molecular_function^3-keto sterol reductase activity`GO:0006696^biological_process^ergosterol biosynthetic process	.	.	.
 TRINITY_DN591_c0_g1	TRINITY_DN591_c0_g1_i1	SYNM_SCHPO^SYNM_SCHPO^Q:1742-738,H:107-441^100%ID^E:0^RecName: Full=Asparagine--tRNA ligase, mitochondrial;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	TRINITY_DN591_c0_g1_i1|m.617	735-1742[-]	SYNM_SCHPO^SYNM_SCHPO^Q:1-335,H:107-441^100%ID^E:0^RecName: Full=Asparagine--tRNA ligase, mitochondrial;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	.	.	.	KEGG:spo:SPBC1198.10c	GO:0005759^cellular_component^mitochondrial matrix`GO:0005739^cellular_component^mitochondrion`GO:0004816^molecular_function^asparagine-tRNA ligase activity`GO:0005524^molecular_function^ATP binding`GO:0000049^molecular_function^tRNA binding`GO:0006421^biological_process^asparaginyl-tRNA aminoacylation`GO:0032543^biological_process^mitochondrial translation	GO:0005759^cellular_component^mitochondrial matrix`GO:0005739^cellular_component^mitochondrion`GO:0004816^molecular_function^asparagine-tRNA ligase activity`GO:0005524^molecular_function^ATP binding`GO:0000049^molecular_function^tRNA binding`GO:0006421^biological_process^asparaginyl-tRNA aminoacylation`GO:0032543^biological_process^mitochondrial translation	.	.	.
 TRINITY_DN591_c0_g1	TRINITY_DN591_c0_g1_i1	SYNM_SCHPO^SYNM_SCHPO^Q:1742-738,H:107-441^100%ID^E:0^RecName: Full=Asparagine--tRNA ligase, mitochondrial;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	TRINITY_DN591_c0_g1_i1|m.618	251-733[+]	UBC16_SCHPO^UBC16_SCHPO^Q:1-160,H:1-160^100%ID^E:2e-116^RecName: Full=Ubiquitin-conjugating enzyme E2 16;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	.	.	.	KEGG:spo:SPBC1198.09	GO:0005759^cellular_component^mitochondrial matrix`GO:0005739^cellular_component^mitochondrion`GO:0004816^molecular_function^asparagine-tRNA ligase activity`GO:0005524^molecular_function^ATP binding`GO:0000049^molecular_function^tRNA binding`GO:0006421^biological_process^asparaginyl-tRNA aminoacylation`GO:0032543^biological_process^mitochondrial translation	GO:0005634^cellular_component^nucleus`GO:0005524^molecular_function^ATP binding`GO:0061631^molecular_function^ubiquitin conjugating enzyme activity`GO:0007031^biological_process^peroxisome organization`GO:0070647^biological_process^protein modification by small protein conjugation or removal`GO:0000209^biological_process^protein polyubiquitination	.	.	.
-TRINITY_DN540_c0_g1	TRINITY_DN540_c0_g1_i1	PPZ_SCHPO^PPZ_SCHPO^Q:26-1567,H:2-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	TRINITY_DN540_c0_g1_i1|m.650	350-1570[+]	PPZ_SCHPO^PPZ_SCHPO^Q:1-406,H:110-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	.	.	.	KEGG:spo:SPAC57A7.08	GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0106306^molecular_function^protein serine phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0106307^molecular_function^protein threonine phosphatase activity`GO:0007165^biological_process^signal transduction	GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0106306^molecular_function^protein serine phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0106307^molecular_function^protein threonine phosphatase activity`GO:0007165^biological_process^signal transduction	.	.	.
-TRINITY_DN540_c0_g2	TRINITY_DN540_c0_g2_i1	PPZ_SCHPO^PPZ_SCHPO^Q:300-1844,H:1-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	TRINITY_DN540_c0_g2_i1|m.651	300-1847[+]	PPZ_SCHPO^PPZ_SCHPO^Q:1-515,H:1-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	.	.	.	KEGG:spo:SPAC57A7.08	GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0106306^molecular_function^protein serine phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0106307^molecular_function^protein threonine phosphatase activity`GO:0007165^biological_process^signal transduction	GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0106306^molecular_function^protein serine phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0106307^molecular_function^protein threonine phosphatase activity`GO:0007165^biological_process^signal transduction	.	.	.
-TRINITY_DN540_c0_g2	TRINITY_DN540_c0_g2_i1	PPZ_SCHPO^PPZ_SCHPO^Q:300-1844,H:1-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	TRINITY_DN540_c0_g2_i1|m.652	1-393[+]	.	.	.	.	.	KEGG:spo:SPAC57A7.08	GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0106306^molecular_function^protein serine phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0106307^molecular_function^protein threonine phosphatase activity`GO:0007165^biological_process^signal transduction	.	.	.	.
+TRINITY_DN540_c0_g1	TRINITY_DN540_c0_g1_i1	PPZ_SCHPO^PPZ_SCHPO^Q:26-1567,H:2-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	TRINITY_DN540_c0_g1_i1|m.650	350-1570[+]	PPZ_SCHPO^PPZ_SCHPO^Q:1-406,H:110-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	.	.	.	KEGG:spo:SPAC57A7.08	GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0007165^biological_process^signal transduction	GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0007165^biological_process^signal transduction	.	.	.
+TRINITY_DN540_c0_g2	TRINITY_DN540_c0_g2_i1	PPZ_SCHPO^PPZ_SCHPO^Q:300-1844,H:1-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	TRINITY_DN540_c0_g2_i1|m.651	300-1847[+]	PPZ_SCHPO^PPZ_SCHPO^Q:1-515,H:1-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	.	.	.	KEGG:spo:SPAC57A7.08	GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0007165^biological_process^signal transduction	GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0007165^biological_process^signal transduction	.	.	.
+TRINITY_DN540_c0_g2	TRINITY_DN540_c0_g2_i1	PPZ_SCHPO^PPZ_SCHPO^Q:300-1844,H:1-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	TRINITY_DN540_c0_g2_i1|m.652	1-393[+]	.	.	.	.	.	KEGG:spo:SPAC57A7.08	GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0007165^biological_process^signal transduction	.	.	.	.
 TRINITY_DN597_c0_g1	TRINITY_DN597_c0_g1_i1	KAPR_SCHPO^KAPR_SCHPO^Q:202-1437,H:1-412^100%ID^E:0^RecName: Full=cAMP-dependent protein kinase regulatory subunit;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	TRINITY_DN597_c0_g1_i1|m.662	202-1440[+]	KAPR_SCHPO^KAPR_SCHPO^Q:1-412,H:1-412^100%ID^E:0^RecName: Full=cAMP-dependent protein kinase regulatory subunit;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	.	.	.	KEGG:spo:SPAC8C9.03	GO:0005952^cellular_component^cAMP-dependent protein kinase complex`GO:0005737^cellular_component^cytoplasm`GO:0005829^cellular_component^cytosol`GO:0005634^cellular_component^nucleus`GO:0030552^molecular_function^cAMP binding`GO:0004862^molecular_function^cAMP-dependent protein kinase inhibitor activity`GO:0008603^molecular_function^cAMP-dependent protein kinase regulator activity`GO:0007189^biological_process^adenylate cyclase-activating G protein-coupled receptor signaling pathway`GO:0042149^biological_process^cellular response to glucose starvation`GO:0110034^biological_process^negative regulation of adenylate cyclase-activating glucose-activated G protein-coupled receptor signaling pathway`GO:0046827^biological_process^positive regulation of protein export from nucleus`GO:0043949^biological_process^regulation of cAMP-mediated signaling`GO:0010738^biological_process^regulation of protein kinase A signaling	GO:0005952^cellular_component^cAMP-dependent protein kinase complex`GO:0005737^cellular_component^cytoplasm`GO:0005829^cellular_component^cytosol`GO:0005634^cellular_component^nucleus`GO:0030552^molecular_function^cAMP binding`GO:0004862^molecular_function^cAMP-dependent protein kinase inhibitor activity`GO:0008603^molecular_function^cAMP-dependent protein kinase regulator activity`GO:0007189^biological_process^adenylate cyclase-activating G protein-coupled receptor signaling pathway`GO:0042149^biological_process^cellular response to glucose starvation`GO:0110034^biological_process^negative regulation of adenylate cyclase-activating glucose-activated G protein-coupled receptor signaling pathway`GO:0046827^biological_process^positive regulation of protein export from nucleus`GO:0043949^biological_process^regulation of cAMP-mediated signaling`GO:0010738^biological_process^regulation of protein kinase A signaling	.	.	.
 TRINITY_DN597_c0_g2	TRINITY_DN597_c0_g2_i1	KAPR_SCHPO^KAPR_SCHPO^Q:202-1437,H:1-412^100%ID^E:0^RecName: Full=cAMP-dependent protein kinase regulatory subunit;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	TRINITY_DN597_c0_g2_i1|m.663	202-1440[+]	KAPR_SCHPO^KAPR_SCHPO^Q:1-412,H:1-412^100%ID^E:0^RecName: Full=cAMP-dependent protein kinase regulatory subunit;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces	.	.	.	.	KEGG:spo:SPAC8C9.03	GO:0005952^cellular_component^cAMP-dependent protein kinase complex`GO:0005737^cellular_component^cytoplasm`GO:0005829^cellular_component^cytosol`GO:0005634^cellular_component^nucleus`GO:0030552^molecular_function^cAMP binding`GO:0004862^molecular_function^cAMP-dependent protein kinase inhibitor activity`GO:0008603^molecular_function^cAMP-dependent protein kinase regulator activity`GO:0007189^biological_process^adenylate cyclase-activating G protein-coupled receptor signaling pathway`GO:0042149^biological_process^cellular response to glucose starvation`GO:0110034^biological_process^negative regulation of adenylate cyclase-activating glucose-activated G protein-coupled receptor signaling pathway`GO:0046827^biological_process^positive regulation of protein export from nucleus`GO:0043949^biological_process^regulation of cAMP-mediated signaling`GO:0010738^biological_process^regulation of protein kinase A signaling	GO:0005952^cellular_component^cAMP-dependent protein kinase complex`GO:0005737^cellular_component^cytoplasm`GO:0005829^cellular_component^cytosol`GO:0005634^cellular_component^nucleus`GO:0030552^molecular_function^cAMP binding`GO:0004862^molecular_function^cAMP-dependent protein kinase inhibitor activity`GO:0008603^molecular_function^cAMP-dependent protein kinase regulator activity`GO:0007189^biological_process^adenylate cyclase-activating G protein-coupled receptor signaling pathway`GO:0042149^biological_process^cellular response to glucose starvation`GO:0110034^biological_process^negative regulation of adenylate cyclase-activating glucose-activated G protein-coupled receptor signaling pathway`GO:0046827^biological_process^positive regulation of protein export from nucleus`GO:0043949^biological_process^regulation of cAMP-mediated signaling`GO:0010738^biological_process^regulation of protein kinase A signaling	.	.	.
 TRINITY_DN547_c0_g1	TRINITY_DN547_c0_g1_i1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.


      

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    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      * Running CMD: wget "http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz"
--2021-12-21 13:41:26--  http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
Resolving ftp.ebi.ac.uk (ftp.ebi.ac.uk)... 193.62.197.74
Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 625798251 (597M) [application/octet-stream]
Saving to: 'uniprot_sprot.dat.gz'

     0K .......... .......... .......... .......... ..........  0% 3.39K 2d2h
    50K .......... .......... .......... .......... ..........  0%  417K 25h15m
   100K ...                                                     0% 23.5M=15s

2021-12-21 13:41:42 (6.94 KB/s) - Connection closed at byte 105788. Retrying.

--2021-12-21 13:41:43--  (try: 2)  http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
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--2021-12-21 13:42:38--  (try: 3)  http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
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--2021-12-21 13:43:40--  (try: 4)  http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected.
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284800K .......... .......... .......... .......... .......... 99% 51.8M 0s
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285000K .......... .......... .......... .......... .......... 99% 50.7M 0s
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285100K .......... .......... .......... .......... .......... 99%  277M 0s
285150K .......... .......... .......... .......... .......... 99% 62.8M 0s
285200K .......... .......... .......... .......... .......... 99%  248M 0s
285250K .......... .......... .......... .......... .......... 99%  253M 0s
285300K .......... .......... .......... .......... .......... 99%  262M 0s
285350K .......... .......... .......... .......... .......... 99% 12.0M 0s
285400K .......... .......... .......... .......... .......... 99% 2.12M 0s
285450K .......... .......... .......... .......... .......... 99%  247M 0s
285500K .......... .......... .......... .......... .......... 99%  259M 0s
285550K .......... .......... .......... .......... .......... 99%  261M 0s
285600K .......... .......... .......... .......... .......... 99%  207M 0s
285650K .......... .......... .......... .......... .......... 99%  275M 0s
285700K .......... .......... .......... .......... .......... 99% 54.1M 0s
285750K .......... .......... .......... .......... .......... 99% 13.3M 0s
285800K .......... .......... .......... .......... .......... 99%  166M 0s
285850K .......... .......... .......... .......... .......... 99% 60.7M 0s
285900K .......... .......... .......... .......... .......... 99%  186M 0s
285950K .......... .......... .......... .......... .......... 99% 83.1M 0s
286000K .......... .......... .......... .......... .......... 99%  170M 0s
286050K .......... .......... .......... .......... .......... 99% 8.26M 0s
286100K .......... .......... .......... ...                  100%  237M=14s

2021-12-21 14:10:28 (20.3 MB/s) - 'Pfam-A.hmm.gz' saved [293000230]

* Running CMD: /usr/local/bin/PFAM_dat_parser.pl Pfam-A.hmm.gz

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[19600]  * Running CMD: /usr/local/bin/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --pfam Pfam-A.hmm.gz.pfam_sqlite_bulk_load
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import Pfam-A.hmm.gz.pfam_sqlite_bulk_load PFAMreference" | sqlite3 Trinotate.sqlite
* Running CMD: wget "http://current.geneontology.org/ontology/external2go/pfam2go" 
--2021-12-21 14:10:59--  http://current.geneontology.org/ontology/external2go/pfam2go
Resolving current.geneontology.org (current.geneontology.org)... 143.204.157.188, 143.204.157.220, 143.204.157.96, ...
Connecting to current.geneontology.org (current.geneontology.org)|143.204.157.188|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 698981 (683K) [text/plain]
Saving to: 'pfam2go'

     0K .......... .......... .......... .......... ..........  7% 13.7M 0s
    50K .......... .......... .......... .......... .......... 14% 7.21M 0s
   100K .......... .......... .......... .......... .......... 21% 13.0M 0s
   150K .......... .......... .......... .......... .......... 29% 15.7M 0s
   200K .......... .......... .......... .......... .......... 36% 17.7M 0s
   250K .......... .......... .......... .......... .......... 43% 27.3M 0s
   300K .......... .......... .......... .......... .......... 51% 21.4M 0s
   350K .......... .......... .......... .......... .......... 58% 26.2M 0s
   400K .......... .......... .......... .......... .......... 65% 50.3M 0s
   450K .......... .......... .......... .......... .......... 73% 42.2M 0s
   500K .......... .......... .......... .......... .......... 80% 37.7M 0s
   550K .......... .......... .......... .......... .......... 87% 42.2M 0s
   600K .......... .......... .......... .......... .......... 95% 42.4M 0s
   650K .......... .......... .......... ..                   100%  140M=0.03s

2021-12-21 14:10:59 (20.9 MB/s) - 'pfam2go' saved [698981/698981]

* Running CMD: /usr/local/bin/PFAMtoGoParser.pl pfam2go > pfam2go.tab
* Running CMD: /usr/local/bin/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --pfam2go pfam2go.tab
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import pfam2go.tab pfam2go" | sqlite3 Trinotate.sqlite
CMD: TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map /corral4/main/objects/b/1/4/dataset_b1441c67-af37-4f06-9a92-e9e489b93fb7.dat --transcript_fasta /corral4/main/objects/7/4/f/dataset_74f49a3b-f8bf-42c0-9072-1e6bdd5ade1f.dat --transdecoder_pep /corral4/main/objects/5/3/c/dataset_53c410f6-44ff-41bd-9a0a-0a7563d1a1e8.dat --bulk_load
-parsing gene/trans map file.... done.
-loading Transcripts.

[100]   
[200]   
done.
-loading ORFs.

done.

CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import tmp.Transcript.bulk_load Transcript" | sqlite3 Trinotate.sqlite
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import tmp.ORF.bulk_load ORF" | sqlite3 Trinotate.sqlite


Loading complete..

CMD: Trinotate_BLAST_loader.pl --sqlite Trinotate.sqlite --outfmt6 /corral4/main/objects/9/9/3/dataset_993670dd-55cc-4ed4-89de-1bb8212b3088.dat --prog blastp --dbtype Swissprot
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import tmp.blast_bulk_load.2593 BlastDbase" | sqlite3 Trinotate.sqlite


BlastDbase loading complete..

CMD: Trinotate_BLAST_loader.pl --sqlite Trinotate.sqlite --outfmt6 /corral4/main/objects/1/1/b/dataset_11baa452-88ef-423d-91d7-76469e29485d.dat --prog blastx --dbtype Swissprot
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import tmp.blast_bulk_load.2775 BlastDbase" | sqlite3 Trinotate.sqlite


BlastDbase loading complete..

CMD: Trinotate_PFAM_loader.pl --sqlite Trinotate.sqlite --pfam /corral4/main/objects/4/a/d/dataset_4add977b-1ac7-4f4f-bde8-2365763bdf68.dat
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import tmp.pfam_bulk_load.2919 HMMERDbase" | sqlite3 Trinotate.sqlite


Loading complete..

CMD: Trinotate_TMHMM_loader.pl --sqlite Trinotate.sqlite --tmhmm /corral4/main/objects/3/3/6/dataset_3368ab1f-8beb-40cf-9509-ceca6d27d651.dat
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import tmp.tmhmm_bulk_load.3108 tmhmm" | sqlite3 Trinotate.sqlite


Loading complete..

CMD: Trinotate_SIGNALP_loader.pl --sqlite Trinotate.sqlite --signalp /corral4/main/objects/b/6/6/dataset_b661a42a-9761-4de8-bf09-7e457f9ca445.dat
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import tmp.signalp_bulk_load.3185 signalp" | sqlite3 Trinotate.sqlite


Loading complete..

CMD: Trinotate_report_writer.pl --sqlite Trinotate.sqlite -E 1e-05 --pfam_cutoff DNC

      

      • 

    

    Standard Output:
    

      

    • 

      memory
memory
memory
memory
memory
memory
memory
memory
memory
memory
memory
memory

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
cond_download
{"__current_case__": 1, "select_download": "yes"}

      

      
report_option
{"E": "1e-05", "incl_pep": "false", "incl_trans": "false", "pfam_cutoff": "DNC"}

      

      
keep_sqlite
"false"

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

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

    Problems:
    

      

    • 

      Output trinotate_out:  different than expected
Expected file size was 573911, actual file size was 573236 (difference of 100 accepted)

      

      • 

    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      * Running CMD: wget "http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz"
--2021-12-21 13:41:26--  http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
Resolving ftp.ebi.ac.uk (ftp.ebi.ac.uk)... 193.62.197.74
Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 625798251 (597M) [application/octet-stream]
Saving to: 'uniprot_sprot.dat.gz'

     0K .......... ...                                          0%  732 =19s

2021-12-21 13:41:46 (732 B/s) - Connection closed at byte 13880. Retrying.

--2021-12-21 13:41:47--  (try: 2)  http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected.
HTTP request sent, awaiting response... 206 Partial Content
Length: 625798251 (597M), 625784371 (597M) remaining [application/octet-stream]
Saving to: 'uniprot_sprot.dat.gz'

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  2550K .......... .......... .......... .......... ..........  0% 5.84K 1h57m
  2600K .......... .......... .......... .......... ..........  0% 1.21M 1h55m
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  3000K .......... .......... .......... .......... ..........  0%  338K 1h43m
  3050K .......... .......... .......... .......... ..........  0% 3.90K 2h23m
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  3150K .......... .......... .......... .......... ..........  0%  416K 2h19m
  3200K .......                                                 0% 92.9M=44s

2021-12-21 13:42:31 (72.9 KB/s) - Connection closed at byte 3284256. Retrying.

--2021-12-21 13:42:33--  (try: 3)  http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected.
HTTP request sent, awaiting response... 206 Partial Content
Length: 625798251 (597M), 622513995 (594M) remaining [application/octet-stream]
Saving to: 'uniprot_sprot.dat.gz'

        [ skipping 3200K ]
  3200K ,,,,,,,... .......... .......... .......... ..........  0% 5.18K 38h7m
  3250K .......... .......... .......... .......... ..........  0% 1.04M 17h39m
  3300K .......... .......... .......... .......... ..........  0%  681K 11h33m
  3350K .......... .......... .......... .......... ..........  0% 6.26K 15h32m
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2021-12-21 13:43:35 (20.7 KB/s) - Connection closed at byte 4580756. Retrying.

--2021-12-21 13:43:38--  (try: 4)  http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected.
HTTP request sent, awaiting response... 206 Partial Content
Length: 625798251 (597M), 621217495 (592M) remaining [application/octet-stream]
Saving to: 'uniprot_sprot.dat.gz'

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2021-12-21 13:43:50 (1.21 KB/s) - Connection closed at byte 4594636. Retrying.

--2021-12-21 13:43:54--  (try: 5)  http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
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HTTP request sent, awaiting response... 206 Partial Content
Length: 625798251 (597M), 621203615 (592M) remaining [application/octet-stream]
Saving to: 'uniprot_sprot.dat.gz'

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2021-12-21 13:45:20 (31.1 KB/s) - Connection closed at byte 7329540. Retrying.

--2021-12-21 13:45:25--  (try: 6)  http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected.
HTTP request sent, awaiting response... 206 Partial Content
Length: 625798251 (597M), 618468711 (590M) remaining [application/octet-stream]
Saving to: 'uniprot_sprot.dat.gz'

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2021-12-21 14:11:19 (22.0 MB/s) - 'Pfam-A.hmm.gz' saved [293000230]

* Running CMD: /usr/local/bin/PFAM_dat_parser.pl Pfam-A.hmm.gz

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[19600]  * Running CMD: /usr/local/bin/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --pfam Pfam-A.hmm.gz.pfam_sqlite_bulk_load
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import Pfam-A.hmm.gz.pfam_sqlite_bulk_load PFAMreference" | sqlite3 Trinotate.sqlite
* Running CMD: wget "http://current.geneontology.org/ontology/external2go/pfam2go" 
--2021-12-21 14:11:51--  http://current.geneontology.org/ontology/external2go/pfam2go
Resolving current.geneontology.org (current.geneontology.org)... 143.204.157.202, 143.204.157.96, 143.204.157.220, ...
Connecting to current.geneontology.org (current.geneontology.org)|143.204.157.202|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 698981 (683K) [text/plain]
Saving to: 'pfam2go'

     0K .......... .......... .......... .......... ..........  7% 13.3M 0s
    50K .......... .......... .......... .......... .......... 14% 6.87M 0s
   100K .......... .......... .......... .......... .......... 21% 15.3M 0s
   150K .......... .......... .......... .......... .......... 29% 14.6M 0s
   200K .......... .......... .......... .......... .......... 36% 22.2M 0s
   250K .......... .......... .......... .......... .......... 43% 25.6M 0s
   300K .......... .......... .......... .......... .......... 51% 18.4M 0s
   350K .......... .......... .......... .......... .......... 58% 46.6M 0s
   400K .......... .......... .......... .......... .......... 65% 28.3M 0s
   450K .......... .......... .......... .......... .......... 73% 43.4M 0s
   500K .......... .......... .......... .......... .......... 80% 54.1M 0s
   550K .......... .......... .......... .......... .......... 87% 34.8M 0s
   600K .......... .......... .......... .......... .......... 95% 56.4M 0s
   650K .......... .......... .......... ..                   100% 52.2M=0.03s

2021-12-21 14:11:51 (21.0 MB/s) - 'pfam2go' saved [698981/698981]

* Running CMD: /usr/local/bin/PFAMtoGoParser.pl pfam2go > pfam2go.tab
* Running CMD: /usr/local/bin/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --pfam2go pfam2go.tab
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import pfam2go.tab pfam2go" | sqlite3 Trinotate.sqlite
CMD: TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map /corral4/main/objects/b/1/4/dataset_b1441c67-af37-4f06-9a92-e9e489b93fb7.dat --transcript_fasta /corral4/main/objects/7/4/f/dataset_74f49a3b-f8bf-42c0-9072-1e6bdd5ade1f.dat --transdecoder_pep /corral4/main/objects/5/3/c/dataset_53c410f6-44ff-41bd-9a0a-0a7563d1a1e8.dat --bulk_load
-parsing gene/trans map file.... done.
-loading Transcripts.

[100]   
[200]   
done.
-loading ORFs.

done.

CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import tmp.Transcript.bulk_load Transcript" | sqlite3 Trinotate.sqlite
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import tmp.ORF.bulk_load ORF" | sqlite3 Trinotate.sqlite


Loading complete..

CMD: Trinotate_BLAST_loader.pl --sqlite Trinotate.sqlite --outfmt6 /corral4/main/objects/9/9/3/dataset_993670dd-55cc-4ed4-89de-1bb8212b3088.dat --prog blastp --dbtype Swissprot
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import tmp.blast_bulk_load.5749 BlastDbase" | sqlite3 Trinotate.sqlite


BlastDbase loading complete..

CMD: Trinotate_BLAST_loader.pl --sqlite Trinotate.sqlite --outfmt6 /corral4/main/objects/1/1/b/dataset_11baa452-88ef-423d-91d7-76469e29485d.dat --prog blastx --dbtype Swissprot
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import tmp.blast_bulk_load.5972 BlastDbase" | sqlite3 Trinotate.sqlite


BlastDbase loading complete..

CMD: Trinotate_PFAM_loader.pl --sqlite Trinotate.sqlite --pfam /corral4/main/objects/4/a/d/dataset_4add977b-1ac7-4f4f-bde8-2365763bdf68.dat
CMD: echo "pragma journal_mode=memory;
pragma synchronous=0;
pragma cache_size=4000000;
.mode tabs
.import tmp.pfam_bulk_load.6199 HMMERDbase" | sqlite3 Trinotate.sqlite


Loading complete..

CMD: Trinotate_report_writer.pl --sqlite Trinotate.sqlite -E 1e-05 --pfam_cutoff DNC --incl_pep --incl_trans

      

      • 

    

    Standard Output:
    

      

    • 

      memory
memory
memory
memory
memory
memory
memory
memory
memory
memory

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
tmhmm
None

      

      
signalp
None

      

      
cond_download
{"__current_case__": 1, "select_download": "yes"}

      

      
report_option
{"E": "1e-05", "incl_pep": "true", "incl_trans": "true", "pfam_cutoff": "DNC"}

      

      
keep_sqlite
"true"

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @natefoo





  


    

      

  

    

        
    
    

  


      
          
  
      
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            natefoo
  

      

      

      commented


        Dec 21, 2021


      
    


  





      


        


  
    

      
          
This is a test data diff error, but the tool runs.

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
            

    

      
    

    


      

          @natefoo
natefoo




            closed this as completed


      Dec 21, 2021

    

  


    


  

  

    
  


  

      

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