Hi,
I'm running SALMON on a local instance and have run into an error when trying to run the program with a Tab delimited file with transcript ID and gene ID separated by Tab (as described in the app). The job will not submit with the file (see trace back below). The program runs fine with the ref file and fastq inputs. There isn't much to the format of the Tab file and the genes and transcripts match the ref (the file was created using the fasta headers). Any help is greatly appreciated.
The server could not complete the request. Please contact the Galaxy Team if this error persists. Unknown error occurred while processing request. { "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.7.2", "tool_version": "0.7.2", "inputs": { "refTranscriptSource|TranscriptSource": "history", "refTranscriptSource|ownFile": { "values": [ { "src": "hda", "keep": false, "hid": 123, "id": "0978e53714b45512", "name": "ToxoDB-32_TgondiiME49_AnnotatedTranscripts.fasta" } ], "batch": false }, "refTranscriptSource|kmerLen": "31", "single_or_paired|single_or_paired_opts": "paired", "single_or_paired|input_mate1": { "values": [ { "src": "hdca", "keep": false, "hid": 120, "id": "5564089c81cf7fe8", "name": "CRK1_minus1_R1" } ], "batch": true }, "single_or_paired|input_mate2": { "values": [ { "src": "hdca", "keep": false, "hid": 121, "id": "ba03619785539f8c", "name": "CRK1_minus1_R2" } ], "batch": true }, "single_or_paired|orientation": "I", "single_or_paired|strandedness": "U", "quasi_orphans|type": "quasi", "perfectHash": "false", "sasamp": "1", "seqBias": "false", "gcBias": "false", "geneMap": { "values": [ { "src": "hda", "keep": false, "hid": 161, "id": "0dd44cc0f0d96662", "name": "SALMON_Transcript_MAP" } ], "batch": false }, "adv|writeMappings": "false", "adv|incompatPrior": "1e-20", "adv|dumpEq": "false", "adv|gcSizeSamp": "1", "adv|biasSpeedSamp": "1", "adv|strictIntersect": "false", "adv|minLen": "19", "adv|sensitive": "false", "adv|consistentHits": "false", "adv|extraSensitive": "false", "adv|coverage": "0.7", "adv|fldMax": "1000", "adv|fldMean": "200", "adv|fldSD": "80", "adv|forgettingFactor": "0.65", "adv|maxOcc": "200", "adv|initUniform": "false", "adv|maxReadOcc": "100", "adv|noEffectiveLengthCorrection": "false", "adv|noFragLengthDist": "false", "adv|noBiasLengthThreshold": "false", "adv|numBiasSamples": "2000000", "adv|numAuxModelSamples": "5000000", "adv|numPreAuxModelSamples": "1000000", "adv|splitWidth": "0", "adv|splitSpanningSeeds": "false", "adv|useVBOpt": "false", "adv|numGibbsSamples": "0", "adv|numBootstraps": "0", "adv|perTranscriptPrior": "false", "adv|vbPrior": "0.001", "adv|writeUnmappedNames": "false" } } Close