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test augustus 3.4.0+galaxy1 #57

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jennaj opened this issue Sep 19, 2022 · 2 comments
Closed

test augustus 3.4.0+galaxy1 #57

jennaj opened this issue Sep 19, 2022 · 2 comments

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@jennaj
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jennaj commented Sep 19, 2022

toolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/3.4.0+galaxy1
@jennaj
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jennaj commented Sep 19, 2022

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/3.4.0+galaxy1

@mvdbeek
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mvdbeek commented Sep 19, 2022

Results (powered by Planemo)

Summary

State Count
Total 6
Passed 6
Error 0
Failure 0
Skipped 0
Passed s
  • ✅ toolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus (Test tool test #1)

    Command Line:

    • 

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
noInFrameStop
"false"

      

      
singlestrand
"false"

      

      
utr
"true"

      

      
model
{"__current_case__": 1, "augustus_mode": "builtin", "organism": "human"}

      

      
softmasking
"false"

      

      
strand
"both"

      

      
genemodel
"complete"

      

      
hints
{"__current_case__": 1, "usehints": "F"}

      

      
range
{"__current_case__": 1, "userange": "F"}

      

      
gff
"false"

      

      
outputs
["protein", "codingseq", "cds"]

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

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

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
noInFrameStop
"false"

      

      
singlestrand
"false"

      

      
utr
"true"

      

      
model
{"__current_case__": 1, "augustus_mode": "builtin", "organism": "human"}

      

      
softmasking
"false"

      

      
strand
"both"

      

      
genemodel
"complete"

      

      
hints
{"__current_case__": 1, "usehints": "F"}

      

      
range
{"__current_case__": 1, "userange": "F"}

      

      
gff
"true"

      

      
outputs
["protein", "codingseq", "cds"]

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

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

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
noInFrameStop
"false"

      

      
singlestrand
"false"

      

      
utr
"false"

      

      
model
{"__current_case__": 1, "augustus_mode": "builtin", "organism": "human"}

      

      
softmasking
"false"

      

      
strand
"both"

      

      
genemodel
"complete"

      

      
hints
{"__current_case__": 1, "usehints": "F"}

      

      
range
{"__current_case__": 1, "userange": "F"}

      

      
gff
"false"

      

      
outputs
["protein", "codingseq", "introns", "cds", "start", "stop"]

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

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

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      # This output was generated with AUGUSTUS (version 3.4.0).
# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# Sources of extrinsic information: M RM E W 
# Setting CDSpart local malus: 0.985
# Setting UTRpart local malus: 0.973
# reading in the file /corral4/main/objects/c/3/9/dataset_c396dd05-e070-48b5-bdc7-6de32bcb286f.dat ...
# Have extrinsic information about 1 sequences (in the specified range). 
# Initializing the parameters using config directory /usr/local/config/ ...
# fly version. Using default transition matrix.
# Looks like /corral4/main/objects/c/7/4/dataset_c746e98e-23d0-4bff-b5e5-aad51535048a.dat is in fasta format.
# We have hints for 1 sequence and for 1 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 9950, name = chr2R) -----
#
# Delete group HintGroup gi|2701440, 8630-8864, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|4203815, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|4245769, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|4245770, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|13769068, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|14693753, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|14695912, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|14699170, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|14700619, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|15539951, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|15543927, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup gi|38623822, 8630-9250, mult= 1, priority= 4 6 features
# Delete group HintGroup SRR023546.8642467/1, 8630-8693, mult= 1, priority= 4 2 features
# Delete group HintGroup gi|2871896, 8811-9250, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|15543159, 8811-9250, mult= 1, priority= 4 4 features
# Delete group HintGroup , 8811-8864, mult= 8, priority= 4 1 features
# Delete group HintGroup , 8811-8864, mult= 8, priority= 4 1 features
# Delete group HintGroup gi|2700091, 9191-9250, mult= 1, priority= 4 2 features
# Delete group HintGroup gi|2701304, 9191-9250, mult= 1, priority= 4 2 features
# Delete group HintGroup gi|2701309, 9191-9250, mult= 1, priority= 4 2 features
# Delete group HintGroup gi|3101873, 9191-9250, mult= 1, priority= 4 2 features
# Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features
# Delete group HintGroup , 9191-9250, mult= 3, priority= 4 1 features
# Deleted 23 groups because some hint was not satisfiable.
# Predicted genes for sequence number 1 on both strands
# start gene chr2R.g1
chr2R	AUGUSTUS	gene	7560	9303	0.84	-	.	chr2R.g1
chr2R	AUGUSTUS	transcript	7560	9303	0.84	-	.	chr2R.g1.t1
chr2R	AUGUSTUS	start_codon	9301	9303	.	-	0	transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1";
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 57.1
# CDS exons: 4/4
#      W:   4 
# CDS introns: 0/3
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 120
#      W: 120 
# incompatible hint groups: 9
#      W:   9 
# end gene chr2R.g1
###
# command line:
# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /corral4/main/objects/c/7/4/dataset_c746e98e-23d0-4bff-b5e5-aad51535048a.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/corral4/main/objects/c/3/9/dataset_c396dd05-e070-48b5-bdc7-6de32bcb286f.dat --extrinsicCfgFile=/corral4/main/objects/9/c/b/dataset_9cb5dae6-4781-4c8b-8b91-9709624d8a75.dat --species=fly

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
noInFrameStop
"false"

      

      
singlestrand
"false"

      

      
utr
"false"

      

      
model
{"__current_case__": 1, "augustus_mode": "builtin", "organism": "fly"}

      

      
softmasking
"false"

      

      
strand
"both"

      

      
genemodel
"complete"

      

      
hints
{"__current_case__": 0, "extrinsiccfg": {"values": [{"id": 102911770, "src": "hda"}]}, "hintsfile": {"values": [{"id": 102911767, "src": "hda"}]}, "usehints": "T"}

      

      
range
{"__current_case__": 1, "userange": "F"}

      

      
gff
"false"

      

      
outputs
[]

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

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

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      # This output was generated with AUGUSTUS (version 3.4.0).
# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# Sources of extrinsic information: M RM E W 
# Setting CDSpart local malus: 0.985
# Setting UTRpart local malus: 0.973
# reading in the file /corral4/main/objects/c/3/9/dataset_c396dd05-e070-48b5-bdc7-6de32bcb286f.dat ...
# Have extrinsic information about 1 sequences (in the specified range). 
# Initializing the parameters using config directory /usr/local/config/ ...
# fly version. Using default transition matrix.
# Looks like /corral4/main/objects/c/7/4/dataset_c746e98e-23d0-4bff-b5e5-aad51535048a.dat is in fasta format.
# We have hints for 1 sequence and for 1 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 2001, name = chr2R) -----
#
# Delete group HintGroup gi|2701440, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|4203815, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|4245769, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|4245770, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|13769068, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|14693753, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|14695912, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|14699170, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|14700619, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|15539951, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|15543927, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup gi|38623822, 1631-1865, mult= 1, priority= 4 4 features
# Delete group HintGroup SRR023546.8642467/1, 1631-1694, mult= 1, priority= 4 2 features
# Delete group HintGroup gi|2871896, 1812-1865, mult= 1, priority= 4 2 features
# Delete group HintGroup gi|15543159, 1812-1865, mult= 1, priority= 4 2 features
# Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features
# Delete group HintGroup , 1812-1865, mult= 8, priority= 4 1 features
# Deleted 17 groups because some hint was not satisfiable.
# Predicted genes for sequence number 1 on both strands
# start gene chr2R.g1
chr2R	AUGUSTUS	gene	7560	8931	0.84	-	.	chr2R.g1
chr2R	AUGUSTUS	transcript	7560	8931	0.84	-	.	chr2R.g1.t1
chr2R	AUGUSTUS	start_codon	8929	8931	.	-	0	transcript_id "chr2R.g1.t1"; gene_id "chr2R.g1";
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 60
# CDS exons: 3/3
#      W:   3 
# CDS introns: 0/2
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 96
#      W:  96 
# incompatible hint groups: 6
#      W:   6 
# end gene chr2R.g1
###
# command line:
# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=off --codingseq=off --introns=off --stop=off --stop=off --cds=off --singlestrand=false /corral4/main/objects/c/7/4/dataset_c746e98e-23d0-4bff-b5e5-aad51535048a.dat --UTR=off --genemodel=complete --softmasking=0 --hintsfile=/corral4/main/objects/c/3/9/dataset_c396dd05-e070-48b5-bdc7-6de32bcb286f.dat --extrinsicCfgFile=/corral4/main/objects/9/c/b/dataset_9cb5dae6-4781-4c8b-8b91-9709624d8a75.dat --predictionStart=7000 --predictionEnd=9000 --species=fly

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
noInFrameStop
"false"

      

      
singlestrand
"false"

      

      
utr
"false"

      

      
model
{"__current_case__": 1, "augustus_mode": "builtin", "organism": "fly"}

      

      
softmasking
"false"

      

      
strand
"both"

      

      
genemodel
"complete"

      

      
hints
{"__current_case__": 0, "extrinsiccfg": {"values": [{"id": 102911770, "src": "hda"}]}, "hintsfile": {"values": [{"id": 102911767, "src": "hda"}]}, "usehints": "T"}

      

      
range
{"__current_case__": 0, "start": "7000", "stop": "9000", "userange": "T"}

      

      
gff
"false"

      

      
outputs
[]

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

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

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      #########################################################################
# WARNING: --softmasking=1 and all sequences are completely in lower case.
# They will be treated as repeatmasked everywhere and genes could be severely underpredicted.
# If this is not intended, rerun with --softmasking=0
#########################################################################

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
noInFrameStop
"false"

      

      
singlestrand
"false"

      

      
utr
"true"

      

      
model
{"__current_case__": 1, "augustus_mode": "builtin", "organism": "human"}

      

      
softmasking
"true"

      

      
strand
"both"

      

      
genemodel
"complete"

      

      
hints
{"__current_case__": 1, "usehints": "F"}

      

      
range
{"__current_case__": 1, "userange": "F"}

      

      
gff
"false"

      

      
outputs
["protein", "codingseq", "cds"]

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
            

    

      
    

    


      

          @jennaj
jennaj




            closed this as completed


      Sep 21, 2022

    

  


    











  
  

    

      

  





  




  
  

              

  
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      2 participants
    

    

        
          @mvdbeek 
        
          @jennaj