test salmon 1.9.0+galaxy2

[jennaj]

toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.9.0+galaxy2

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.9.0+galaxy2

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	11
Passed	5
Error	2
Failure	4
Skipped	0

Errored s

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test tool test #1)

  Execution Problem:

  • parameter 'input_mate2': the previously selected dataset has entered an unusable state
    

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test Test racon 1.3.1.1 #11)

  Execution Problem:

  • Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .
    

Failed s

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test test against test.galaxyproject.org #2)

  Problems:

  • 'command_line'
    

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)

  Problems:

  • Standard error of the job different than expected
    Expected text 'Sampling alignments; outputting results to ./output/postSample.bam' in output ('')
    

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    quant_type	{"__current_case__": 1, "afile": {"values": [{"id": 108637704, "src": "hda"}]}, "discardOrphans": false, "gencode": false, "libtype": {"__current_case__": 0, "strandedness": "A"}, "noErrorModel": true, "numErrorBins": "5", "ont": false, "qtype": "alignment", "sampleOut": true, "sampleUnaligned": true, "transcript": {"values": [{"id": 108637681, "src": "hda"}]}}
    geneMap	None
    seqBias	false
    gcBias	false
    incompatPrior	"0.0"
    meta	false
    adv	{"biasSpeedSamp": "5", "bootstrapReproject": false, "dumpEq": false, "dumpEqWeights": false, "fldMax": "1000", "fldMean": "250", "fldSD": "25", "forgettingFactor": "0.65", "initUniform": false, "maxReadOcc": "100", "minAssignedFrags": "", "noBiasLengthThreshold": false, "noEffectiveLengthCorrection": false, "noFragLengthDist": false, "noGammaDraw": false, "noLengthCorrection": false, "numAuxModelSamples": "5000000", "numBiasSamples": "2000000", "numBootstraps": "0", "numGibbsSamples": "0", "numPreAuxModelSamples": "5000", "perTranscriptPrior": false, "rangeFactorizationBins": "0", "sigDigits": "3", "skipQuant": false, "thinningFactor": "16", "useEM": false, "vbPrior": "1e-05", "writeOrphanLinks": false, "writeUnmappedNames": false}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test Test trinotate 3.2.2+galaxy0 #6)

  Problems:

  • 'command_line'
    

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test Test trim_galore 0.6.7+galaxy0 #10)

  Problems:

  • 'command_line'
    

Passed s

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

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    quant_type	{"__current_case__": 0, "bam_options": {"__current_case__": 1, "writeMappings": ""}, "consensusSlack": "0", "consistentHits": false, "discardOrphansQuasi": false, "dovetail": false, "input": {"single_or_paired": {"__current_case__": 0, "input_singles": {"values": [{"id": 108637681, "src": "hda"}]}, "libtype": {"__current_case__": 0, "strandedness": "A"}, "single_or_paired_opts": "single"}}, "qtype": "reads", "quasiCoverage": "", "recoverOrphans": false, "refTranscriptSource": {"TranscriptSource": "history", "__current_case__": 1, "s_index": {"fasta": {"values": [{"id": 108637681, "src": "hda"}]}, "genome": null, "kmer": "31", "phash": false}}, "type": "quasi", "validmap": {"__current_case__": 1, "validateMappings": false}}
    geneMap	None
    seqBias	false
    gcBias	false
    incompatPrior	"0.0"
    meta	false
    adv	{"biasSpeedSamp": "5", "bootstrapReproject": false, "dumpEq": false, "dumpEqWeights": false, "fldMax": "1000", "fldMean": "250", "fldSD": "25", "forgettingFactor": "0.65", "initUniform": false, "maxReadOcc": "100", "minAssignedFrags": "", "noBiasLengthThreshold": false, "noEffectiveLengthCorrection": false, "noFragLengthDist": false, "noGammaDraw": false, "noLengthCorrection": false, "numAuxModelSamples": "5000000", "numBiasSamples": "2000000", "numBootstraps": "0", "numGibbsSamples": "0", "numPreAuxModelSamples": "5000", "perTranscriptPrior": false, "rangeFactorizationBins": "0", "sigDigits": "3", "skipQuant": false, "thinningFactor": "16", "useEM": false, "vbPrior": "1e-05", "writeOrphanLinks": false, "writeUnmappedNames": false}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

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

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    quant_type	{"__current_case__": 0, "bam_options": {"__current_case__": 1, "writeMappings": ""}, "consensusSlack": "0", "consistentHits": false, "discardOrphansQuasi": false, "dovetail": false, "input": {"single_or_paired": {"__current_case__": 0, "input_singles": {"values": [{"id": 108637681, "src": "hda"}]}, "libtype": {"__current_case__": 0, "strandedness": "A"}, "single_or_paired_opts": "single"}}, "qtype": "reads", "quasiCoverage": "", "recoverOrphans": false, "refTranscriptSource": {"TranscriptSource": "history", "__current_case__": 1, "s_index": {"fasta": {"values": [{"id": 108637681, "src": "hda"}]}, "genome": null, "kmer": "31", "phash": false}}, "type": "quasi", "validmap": {"__current_case__": 1, "validateMappings": false}}
    geneMap	None
    seqBias	false
    gcBias	false
    incompatPrior	"0.0"
    meta	false
    adv	{"biasSpeedSamp": "5", "bootstrapReproject": false, "dumpEq": false, "dumpEqWeights": false, "fldMax": "1000", "fldMean": "250", "fldSD": "25", "forgettingFactor": "0.65", "initUniform": false, "maxReadOcc": "100", "minAssignedFrags": "", "noBiasLengthThreshold": false, "noEffectiveLengthCorrection": false, "noFragLengthDist": false, "noGammaDraw": false, "noLengthCorrection": false, "numAuxModelSamples": "5000000", "numBiasSamples": "2000000", "numBootstraps": "0", "numGibbsSamples": "0", "numPreAuxModelSamples": "5000", "perTranscriptPrior": false, "rangeFactorizationBins": "0", "sigDigits": "3", "skipQuant": false, "thinningFactor": "16", "useEM": false, "vbPrior": "1e-05", "writeOrphanLinks": false, "writeUnmappedNames": false}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test Test pangolin 3.1.17+galaxy1 #7)

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    quant_type	{"__current_case__": 0, "bam_options": {"__current_case__": 1, "writeMappings": ""}, "consensusSlack": "0", "consistentHits": false, "discardOrphansQuasi": false, "dovetail": true, "input": {"single_or_paired": {"__current_case__": 0, "input_singles": {"values": [{"id": 108637681, "src": "hda"}]}, "libtype": {"__current_case__": 0, "strandedness": "A"}, "single_or_paired_opts": "single"}}, "qtype": "reads", "quasiCoverage": "", "recoverOrphans": true, "refTranscriptSource": {"TranscriptSource": "history", "__current_case__": 1, "s_index": {"fasta": {"values": [{"id": 108637681, "src": "hda"}]}, "genome": null, "kmer": "31", "phash": false}}, "type": "quasi", "validmap": {"__current_case__": 0, "gapExtensionPenalty": "3", "gapOpenPenalty": "5", "hardFilter": false, "matchScore": "2", "maxMMPExtension": "", "mimicBT2": false, "mimicStrictBT2": false, "minScoreFraction": "0.65", "mismatchPenalty": "4", "validateMappings": true}}
    geneMap	None
    seqBias	false
    gcBias	false
    incompatPrior	"0.0"
    meta	false
    adv	{"biasSpeedSamp": "5", "bootstrapReproject": false, "dumpEq": false, "dumpEqWeights": false, "fldMax": "1000", "fldMean": "250", "fldSD": "25", "forgettingFactor": "0.65", "initUniform": false, "maxReadOcc": "100", "minAssignedFrags": "", "noBiasLengthThreshold": false, "noEffectiveLengthCorrection": false, "noFragLengthDist": false, "noGammaDraw": false, "noLengthCorrection": false, "numAuxModelSamples": "5000000", "numBiasSamples": "2000000", "numBootstraps": "0", "numGibbsSamples": "0", "numPreAuxModelSamples": "5000", "perTranscriptPrior": false, "rangeFactorizationBins": "0", "sigDigits": "3", "skipQuant": false, "thinningFactor": "16", "useEM": false, "vbPrior": "1e-05", "writeOrphanLinks": false, "writeUnmappedNames": false}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test Test SEACR 1.3+galaxy1 on usegalaxy.org #8)

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    quant_type	{"__current_case__": 0, "bam_options": {"__current_case__": 1, "writeMappings": ""}, "consensusSlack": "0", "consistentHits": false, "discardOrphansQuasi": false, "dovetail": false, "input": {"single_or_paired": {"__current_case__": 0, "input_singles": {"values": [{"id": 108637683, "src": "hda"}]}, "libtype": {"__current_case__": 0, "strandedness": "A"}, "single_or_paired_opts": "single"}}, "qtype": "reads", "quasiCoverage": "", "recoverOrphans": false, "refTranscriptSource": {"TranscriptSource": "history", "__current_case__": 1, "s_index": {"fasta": {"values": [{"id": 108637681, "src": "hda"}]}, "genome": null, "kmer": "31", "phash": false}}, "type": "quasi", "validmap": {"__current_case__": 1, "validateMappings": false}}
    geneMap	None
    seqBias	true
    gcBias	true
    incompatPrior	"0.0"
    meta	false
    adv	{"biasSpeedSamp": "5", "bootstrapReproject": false, "dumpEq": true, "dumpEqWeights": false, "fldMax": "1000", "fldMean": "250", "fldSD": "25", "forgettingFactor": "0.65", "initUniform": true, "maxReadOcc": "100", "minAssignedFrags": "10", "noBiasLengthThreshold": false, "noEffectiveLengthCorrection": false, "noFragLengthDist": false, "noGammaDraw": true, "noLengthCorrection": false, "numAuxModelSamples": "5000000", "numBiasSamples": "2000000", "numBootstraps": "0", "numGibbsSamples": "0", "numPreAuxModelSamples": "5000", "perTranscriptPrior": false, "rangeFactorizationBins": "0", "sigDigits": "3", "skipQuant": false, "thinningFactor": "16", "useEM": true, "vbPrior": "1e-05", "writeOrphanLinks": false, "writeUnmappedNames": false}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.9.0+galaxy2

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	11
Passed	3
Error	0
Failure	8
Skipped	0

Failed s

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test tool test #1)

  Problems:

  • 'command_line'
    

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test test against test.galaxyproject.org #2)

  Problems:

  • 'command_line'
    

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test Test racon 1.3.1.1 #11)

  Problems:

  • 'command_line'
    

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)

  Problems:

  • Standard error of the job different than expected
    Expected text 'Sampling alignments; outputting results to ./output/postSample.bam' in output ('')
    

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    quant_type	{"__current_case__": 1, "afile": {"values": [{"id": 108640605, "src": "hda"}]}, "discardOrphans": false, "gencode": false, "libtype": {"__current_case__": 0, "strandedness": "A"}, "noErrorModel": true, "numErrorBins": "5", "ont": false, "qtype": "alignment", "sampleOut": true, "sampleUnaligned": true, "transcript": {"values": [{"id": 108640593, "src": "hda"}]}}
    geneMap	None
    seqBias	false
    gcBias	false
    incompatPrior	"0.0"
    meta	false
    adv	{"biasSpeedSamp": "5", "bootstrapReproject": false, "dumpEq": false, "dumpEqWeights": false, "fldMax": "1000", "fldMean": "250", "fldSD": "25", "forgettingFactor": "0.65", "initUniform": false, "maxReadOcc": "100", "minAssignedFrags": "", "noBiasLengthThreshold": false, "noEffectiveLengthCorrection": false, "noFragLengthDist": false, "noGammaDraw": false, "noLengthCorrection": false, "numAuxModelSamples": "5000000", "numBiasSamples": "2000000", "numBootstraps": "0", "numGibbsSamples": "0", "numPreAuxModelSamples": "5000", "perTranscriptPrior": false, "rangeFactorizationBins": "0", "sigDigits": "3", "skipQuant": false, "thinningFactor": "16", "useEM": false, "vbPrior": "1e-05", "writeOrphanLinks": false, "writeUnmappedNames": false}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test Test trinotate 3.2.2+galaxy0 #6)

  Problems:

  • 'command_line'
    

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test Test pangolin 3.1.17+galaxy1 #7)

  Problems:

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.9.0+galaxy2, exit_code: 1, stderr: .
    

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.9.0+galaxy2, exit_code: 1, stderr: .
    

  Command Line:

  Exit Code:

  • 1

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    quant_type	{"__current_case__": 0, "bam_options": {"__current_case__": 1, "writeMappings": ""}, "consensusSlack": "0", "consistentHits": false, "discardOrphansQuasi": false, "dovetail": true, "input": {"single_or_paired": {"__current_case__": 0, "input_singles": {"values": [{"id": 108640595, "src": "hda"}]}, "libtype": {"__current_case__": 0, "strandedness": "A"}, "single_or_paired_opts": "single"}}, "qtype": "reads", "quasiCoverage": "", "recoverOrphans": true, "refTranscriptSource": {"TranscriptSource": "history", "__current_case__": 1, "s_index": {"fasta": {"values": [{"id": 108640593, "src": "hda"}]}, "genome": null, "kmer": "31", "phash": false}}, "type": "quasi", "validmap": {"__current_case__": 0, "gapExtensionPenalty": "3", "gapOpenPenalty": "5", "hardFilter": false, "matchScore": "2", "maxMMPExtension": "", "mimicBT2": false, "mimicStrictBT2": false, "minScoreFraction": "0.65", "mismatchPenalty": "4", "validateMappings": true}}
    geneMap	None
    seqBias	false
    gcBias	false
    incompatPrior	"0.0"
    meta	false
    adv	{"biasSpeedSamp": "5", "bootstrapReproject": false, "dumpEq": false, "dumpEqWeights": false, "fldMax": "1000", "fldMean": "250", "fldSD": "25", "forgettingFactor": "0.65", "initUniform": false, "maxReadOcc": "100", "minAssignedFrags": "", "noBiasLengthThreshold": false, "noEffectiveLengthCorrection": false, "noFragLengthDist": false, "noGammaDraw": false, "noLengthCorrection": false, "numAuxModelSamples": "5000000", "numBiasSamples": "2000000", "numBootstraps": "0", "numGibbsSamples": "0", "numPreAuxModelSamples": "5000", "perTranscriptPrior": false, "rangeFactorizationBins": "0", "sigDigits": "3", "skipQuant": false, "thinningFactor": "16", "useEM": false, "vbPrior": "1e-05", "writeOrphanLinks": false, "writeUnmappedNames": false}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test Test SEACR 1.3+galaxy1 on usegalaxy.org #8)

  Problems:

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.9.0+galaxy2, exit_code: 1, stderr: .
    

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.9.0+galaxy2, exit_code: 1, stderr: .
    

  Command Line:

  Exit Code:

  • 1

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    quant_type	{"__current_case__": 0, "bam_options": {"__current_case__": 1, "writeMappings": ""}, "consensusSlack": "0", "consistentHits": false, "discardOrphansQuasi": false, "dovetail": false, "input": {"single_or_paired": {"__current_case__": 0, "input_singles": {"values": [{"id": 108640595, "src": "hda"}]}, "libtype": {"__current_case__": 0, "strandedness": "A"}, "single_or_paired_opts": "single"}}, "qtype": "reads", "quasiCoverage": "", "recoverOrphans": false, "refTranscriptSource": {"TranscriptSource": "history", "__current_case__": 1, "s_index": {"fasta": {"values": [{"id": 108640593, "src": "hda"}]}, "genome": null, "kmer": "31", "phash": false}}, "type": "quasi", "validmap": {"__current_case__": 1, "validateMappings": false}}
    geneMap	None
    seqBias	true
    gcBias	true
    incompatPrior	"0.0"
    meta	false
    adv	{"biasSpeedSamp": "5", "bootstrapReproject": false, "dumpEq": true, "dumpEqWeights": false, "fldMax": "1000", "fldMean": "250", "fldSD": "25", "forgettingFactor": "0.65", "initUniform": true, "maxReadOcc": "100", "minAssignedFrags": "10", "noBiasLengthThreshold": false, "noEffectiveLengthCorrection": false, "noFragLengthDist": false, "noGammaDraw": true, "noLengthCorrection": false, "numAuxModelSamples": "5000000", "numBiasSamples": "2000000", "numBootstraps": "0", "numGibbsSamples": "0", "numPreAuxModelSamples": "5000", "perTranscriptPrior": false, "rangeFactorizationBins": "0", "sigDigits": "3", "skipQuant": false, "thinningFactor": "16", "useEM": true, "vbPrior": "1e-05", "writeOrphanLinks": false, "writeUnmappedNames": false}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test Test trim_galore 0.6.7+galaxy0 #10)

  Problems:

  • 'command_line'
    

Passed s

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

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    quant_type	{"__current_case__": 0, "bam_options": {"__current_case__": 1, "writeMappings": ""}, "consensusSlack": "0", "consistentHits": false, "discardOrphansQuasi": false, "dovetail": false, "input": {"single_or_paired": {"__current_case__": 0, "input_singles": {"values": [{"id": 108640593, "src": "hda"}]}, "libtype": {"__current_case__": 0, "strandedness": "A"}, "single_or_paired_opts": "single"}}, "qtype": "reads", "quasiCoverage": "", "recoverOrphans": false, "refTranscriptSource": {"TranscriptSource": "history", "__current_case__": 1, "s_index": {"fasta": {"values": [{"id": 108640593, "src": "hda"}]}, "genome": null, "kmer": "31", "phash": false}}, "type": "quasi", "validmap": {"__current_case__": 1, "validateMappings": false}}
    geneMap	None
    seqBias	false
    gcBias	false
    incompatPrior	"0.0"
    meta	false
    adv	{"biasSpeedSamp": "5", "bootstrapReproject": false, "dumpEq": false, "dumpEqWeights": false, "fldMax": "1000", "fldMean": "250", "fldSD": "25", "forgettingFactor": "0.65", "initUniform": false, "maxReadOcc": "100", "minAssignedFrags": "", "noBiasLengthThreshold": false, "noEffectiveLengthCorrection": false, "noFragLengthDist": false, "noGammaDraw": false, "noLengthCorrection": false, "numAuxModelSamples": "5000000", "numBiasSamples": "2000000", "numBootstraps": "0", "numGibbsSamples": "0", "numPreAuxModelSamples": "5000", "perTranscriptPrior": false, "rangeFactorizationBins": "0", "sigDigits": "3", "skipQuant": false, "thinningFactor": "16", "useEM": false, "vbPrior": "1e-05", "writeOrphanLinks": false, "writeUnmappedNames": false}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

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

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    quant_type	{"__current_case__": 0, "bam_options": {"__current_case__": 1, "writeMappings": ""}, "consensusSlack": "0", "consistentHits": false, "discardOrphansQuasi": false, "dovetail": false, "input": {"single_or_paired": {"__current_case__": 0, "input_singles": {"values": [{"id": 108640599, "src": "hda"}]}, "libtype": {"__current_case__": 0, "strandedness": "A"}, "single_or_paired_opts": "single"}}, "qtype": "reads", "quasiCoverage": "", "recoverOrphans": false, "refTranscriptSource": {"TranscriptSource": "history", "__current_case__": 1, "s_index": {"fasta": {"values": [{"id": 108640593, "src": "hda"}]}, "genome": null, "kmer": "31", "phash": false}}, "type": "quasi", "validmap": {"__current_case__": 1, "validateMappings": false}}
    geneMap	None
    seqBias	false
    gcBias	false
    incompatPrior	"0.0"
    meta	false
    adv	{"biasSpeedSamp": "5", "bootstrapReproject": false, "dumpEq": false, "dumpEqWeights": false, "fldMax": "1000", "fldMean": "250", "fldSD": "25", "forgettingFactor": "0.65", "initUniform": false, "maxReadOcc": "100", "minAssignedFrags": "", "noBiasLengthThreshold": false, "noEffectiveLengthCorrection": false, "noFragLengthDist": false, "noGammaDraw": false, "noLengthCorrection": false, "numAuxModelSamples": "5000000", "numBiasSamples": "2000000", "numBootstraps": "0", "numGibbsSamples": "0", "numPreAuxModelSamples": "5000", "perTranscriptPrior": false, "rangeFactorizationBins": "0", "sigDigits": "3", "skipQuant": false, "thinningFactor": "16", "useEM": false, "vbPrior": "1e-05", "writeOrphanLinks": false, "writeUnmappedNames": false}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.9.0+galaxy2

[jennaj]

Not sure what this means yet

Failed s
❌ toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon (Test #1)
Problems:

'command_line'