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"mergeSetPeptidetable" process error with "NA" value #10

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TnakaNY opened this issue Jan 2, 2020 · 18 comments
Open

"mergeSetPeptidetable" process error with "NA" value #10

TnakaNY opened this issue Jan 2, 2020 · 18 comments

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@TnakaNY
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TnakaNY commented Jan 2, 2020

I am trying to run this variant peptide detection pipeline.
It worked without any error when i ran this pipeline within 2 proteome file.
But, when i ran this pipeline with 4 mzml files, pipeline stopped with some error at final step called "mergeSetPeptidetable".

It seemed that "NA" value just caused this error. I am not sure, but it looks it does not matter for final result.

I attached all terminal text below with error message. Could anyone help me?

(base) tana1@tana1-VirtualBox:~/workspace/workflow13$ sudo nextflow run main.nf --tdb /home/tana1/workspace/varDB/VarDB.fasta --mzmls /home/tana1/workspace/data/test2/*.mzML --activation hcd --gtf /home/tana1/workspace/varDB/VarDB.gtf --mods /home/tana1/workspace/mods/MSGFPlus_Mods_FFPEv1.txt --knownproteins /home/tana1/workspace/ensembl/Homo_sapiens.GRCh38.pep.all.fa --blastdb /home/tana1/workspace/varDB/UniProteome+Ensembl87+refseq+GENCODE24.proteins.fasta --cosmic /home/tana1/workspace/cosmic/CosmicMutantExport.tsv --snpfa /home/tana1/workspace/varDB/MSCanProVar_ensemblV79.filtered.fasta --genome /home/tana1/workspace/hg19/hg19.chr1-22.X.Y.M.fa.masked --dbsnp /home/tana1/workspace/varDB/snp151CodingDbSnp.txt --annovar_dir /home/tana1/workspace/annovar/annovar --bigwigs /home/tana1/workspace/bigwig --outdir /home/tana1/workspace/result13 -profile docker,standard
[sudo] password for tana1:
N E X T F L O W ~ version 19.10.0
Launching main.nf [intergalactic_mandelbrot] - revision: 6ff5d47fa2
4 mzML files in analysis
Detected setnames: NA
executor > local (1)
executor > local (3)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [ 0%] 0 of 1
[- ] process > concatFasta -
[97/1e08f0] process > makeProtSeq [ 0%] 0 of 1
[88/6a32b9] process > makeTrypSeq [ 0%] 0 of 1
[- ] process > IsobaricQuant -
[- ] process > createSpectraLookup -
[- ] process > msgfPlus -
[- ] process > percolator -
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
[- ] process > filterPercolator -
[- ] process > svmToTSV -
[- ] process > createPSMTables -
executor > local (4)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [ 0%] 0 of 1
[- ] process > concatFasta -
[97/1e08f0] process > makeProtSeq [ 0%] 0 of 1
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [ 0%] 0 of 1
[- ] process > msgfPlus -
[- ] process > percolator -
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
[- ] process > filterPercolator -
[- ] process > svmToTSV -
[- ] process > createPSMTables -
executor > local (4)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [ 0%] 0 of 1
[- ] process > concatFasta -
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [ 0%] 0 of 1
[- ] process > msgfPlus -
[- ] process > percolator -
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
[- ] process > filterPercolator -
[- ] process > svmToTSV -
executor > local (4)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [ 0%] 0 of 1
[- ] process > concatFasta -
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[- ] process > msgfPlus -
[- ] process > percolator -
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
executor > local (5)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [ 0%] 0 of 1
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[- ] process > msgfPlus -
[- ] process > percolator -
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
executor > local (5)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[- ] process > msgfPlus -
[- ] process > percolator -
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
executor > local (8)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[01/dcce1d] process > msgfPlus (1) [ 0%] 0 of 3
[- ] process > percolator -
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
executor > local (9)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [ 25%] 1 of 4
[- ] process > percolator -
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
executor > local (9)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[01/dcce1d] process > msgfPlus (1) [ 50%] 2 of 4
[- ] process > percolator -
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
executor > local (9)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ae/700c89] process > msgfPlus (4) [ 75%] 3 of 4
[- ] process > percolator -
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
executor > local (10)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [ 0%] 0 of 1
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
executor > local (10)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
executor > local (12)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [ 0%] 0 of 1
[c3/6d3c65] process > getNovelPercolator (1) [ 0%] 0 of 1
executor > local (12)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [ 0%] 0 of 1
executor > local (12)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (14)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (15)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (16)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (17)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (19)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (20)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (20)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (21)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (21)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (23)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
[1b/9b48b3] process > filterPercolator (1) [100%] 2 of 2 ✔
[84/66b904] process > svmToTSV (2) [100%] 2 of 2 ✔
Pipeline output ready: /home/tana1/workspace/workflow13/work/ae/5f8601cc4c4c5b8877f2a33ed19250/variant_psmtable.txtble (2) [ 0%] 0 of 2
executor > local (24)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (24)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (24)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (25)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (27)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (28)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (29)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (30)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (31)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (32)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (33)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (34)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (35)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (36)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (37)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (37)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (37)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
executor > local (38)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
[1b/9b48b3] process > filterPercolator (1) [100%] 2 of 2 ✔
[84/66b904] process > svmToTSV (2) [100%] 2 of 2 ✔
[ff/db734c] process > createPSMTables (2) [100%] 2 of 2 ✔
[ae/5f8601] process > mergeSetPSMtable (1) [100%] 2 of 2 ✔
[23/f7f7df] process > prePeptideTable (2) [100%] 2 of 2 ✔
[30/3fec5d] process > createFastaBedGFF (1) [100%] 1 of 1 ✔
[60/299c1a] process > BlastPNovel (1) [100%] 1 of 1 ✔
[3d/fdfdb5] process > ParseBlastpOut (1) [100%] 1 of 1 ✔
[80/455017] process > ValidateSingleMismatchNovpeps (1) [100%] 1 of 1 ✔
executor > local (38)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
[1b/9b48b3] process > filterPercolator (1) [100%] 2 of 2 ✔
[84/66b904] process > svmToTSV (2) [100%] 2 of 2 ✔
[ff/db734c] process > createPSMTables (2) [100%] 2 of 2 ✔
[ae/5f8601] process > mergeSetPSMtable (1) [100%] 2 of 2 ✔
[23/f7f7df] process > prePeptideTable (2) [100%] 2 of 2 ✔
[30/3fec5d] process > createFastaBedGFF (1) [100%] 1 of 1 ✔
[60/299c1a] process > BlastPNovel (1) [100%] 1 of 1 ✔
[3d/fdfdb5] process > ParseBlastpOut (1) [100%] 1 of 1 ✔
[80/455017] process > ValidateSingleMismatchNovpeps (1) [100%] 1 of 1 ✔
executor > local (40)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
[1b/9b48b3] process > filterPercolator (1) [100%] 2 of 2 ✔
[84/66b904] process > svmToTSV (2) [100%] 2 of 2 ✔
[ff/db734c] process > createPSMTables (2) [100%] 2 of 2 ✔
[ae/5f8601] process > mergeSetPSMtable (1) [100%] 2 of 2 ✔
[23/f7f7df] process > prePeptideTable (2) [100%] 2 of 2 ✔
[30/3fec5d] process > createFastaBedGFF (1) [100%] 1 of 1 ✔
[60/299c1a] process > BlastPNovel (1) [100%] 1 of 1 ✔
[3d/fdfdb5] process > ParseBlastpOut (1) [100%] 1 of 1 ✔
[80/455017] process > ValidateSingleMismatchNovpeps (1) [100%] 1 of 1 ✔
[d3/75c83e] process > novpepSpecAIOutParse (1) [100%] 1 of 1 ✔
[af/63688c] process > BLATNovel (1) [100%] 1 of 1 ✔
executor > local (40)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
[1b/9b48b3] process > filterPercolator (1) [100%] 2 of 2 ✔
[84/66b904] process > svmToTSV (2) [100%] 2 of 2 ✔
[ff/db734c] process > createPSMTables (2) [100%] 2 of 2 ✔
[ae/5f8601] process > mergeSetPSMtable (1) [100%] 2 of 2 ✔
[23/f7f7df] process > prePeptideTable (2) [100%] 2 of 2 ✔
[30/3fec5d] process > createFastaBedGFF (1) [100%] 1 of 1 ✔
[60/299c1a] process > BlastPNovel (1) [100%] 1 of 1 ✔
[3d/fdfdb5] process > ParseBlastpOut (1) [100%] 1 of 1 ✔
[80/455017] process > ValidateSingleMismatchNovpeps (1) [100%] 1 of 1 ✔
executor > local (40)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
[1b/9b48b3] process > filterPercolator (1) [100%] 2 of 2 ✔
[84/66b904] process > svmToTSV (2) [100%] 2 of 2 ✔
[ff/db734c] process > createPSMTables (2) [100%] 2 of 2 ✔
[ae/5f8601] process > mergeSetPSMtable (1) [100%] 2 of 2 ✔
[23/f7f7df] process > prePeptideTable (2) [100%] 2 of 2 ✔
[30/3fec5d] process > createFastaBedGFF (1) [100%] 1 of 1 ✔
[60/299c1a] process > BlastPNovel (1) [100%] 1 of 1 ✔
[3d/fdfdb5] process > ParseBlastpOut (1) [100%] 1 of 1 ✔
[80/455017] process > ValidateSingleMismatchNovpeps (1) [100%] 1 of 1 ✔
[d3/75c83e] process > novpepSpecAIOutParse (1) [100%] 1 of 1 ✔
[af/63688c] process > BLATNovel (1) [100%] 1 of 1 ✔
[21/048bfb] process > parseBLATout (1) [100%] 1 of 1 ✔
[f9/4f1ee6] process > labelnsSNP (1) [100%] 1 of 1 ✔
[f8/7770a6] process > phastcons (1) [100%] 1 of 1 ✔
[ce/880aaa] process > phyloCSF (1) [100%] 1 of 1 ✔
[- ] process > scanBams -
[66/026dad] process > annovar (1) [100%] 1 of 1 ✔
[d1/944bac] process > parseAnnovarOut (1) [100%] 1 of 1 ✔
[4c/5230be] process > combineResults (1) [100%] 1 of 1 ✔
[f8/61a7ff] process > prepSpectrumAI (1) [100%] 1 of 1 ✔
[d1/b95be3] process > SpectrumAI (1) [100%] 1 of 1 ✔
[54/a5a93e] process > mapVariantPeptidesToGenome (1) [100%] 1 of 1 ✔
[5b/03e42c] process > mergeSetPeptidetable (2) [ 50%] 1 of 2
WARN: Input tuple does not match input set cardinality declared by process combineResults -- offending value: [NA, /home/tana1/workspace/workflow13/work/f9/4f1ee6d02958ecde7615471292f5f3/nssnp.txt, /home/tana1/workspace/workflow13/work/d3/75c83e3c86c72fa583b9845477da55/novpep_specai.txt, /home/tana1/workspace/workflow13/work/21/048bfb80a397530b8ac253672cda6d/peptable_blat.txt, /home/tana1/workspace/workflow13/work/d1/944bac9c54df77706702fba00275ea/parsed_annovar.txt, /home/tana1/workspace/workflow13/work/f8/7770a6ad76319e6240704f100a5e2f/phastcons.txt, /home/tana1/workspace/workflow13/work/ce/880aaaf707413e3e154a788f2542cb/phylocsf.txt, /home/tana1/workspace/workflow13/work/30/3fec5d0e9a85149ee9b56ac64aff02/novpep_perco_quant.txt]
Error executing process > 'mergeSetPeptidetable (1)'

Caused by:
Process mergeSetPeptidetable (1) terminated with an error exit status (1)

Command executed:

build non-changing fields (seq based fields) table:

fixfields=head -n1 peps1 |tr -s '\t' '\n' | egrep -vn '(Setname|Spectrum|q-val|plex|Bare peptide)' | cut -f 1 -d ':'
fixfields=echo $fixfields | sed 's/ /,/g'
head -n1 peps1 | cut -f echo $fixfields > fixheader
count=1; for setn in NA ; do
cut -f echo $fixfields peps$count | tail -n+2 >> fixpeps
((count++))
done
if [ nov == 'nov' ]
then
cat fixheader <(sort -u -k1b,1 fixpeps) > temp
group_novpepToLoci.py --input temp --output temp.loci --distance 10kb
head -n1 temp.loci > fixheader
tail -n+2 temp.loci > fixpeps
fi
sort -u -k1b,1 fixpeps > temp
mv temp fixpeps

Build changing fields table

touch peptable
count=1; for setn in NA; do
varfields=head -n1 peps$count |tr -s '\t' '\n' | egrep -n '(Peptide|Spectrum|q-val|plex)' | cut -f 1 -d ':'
varfields=echo $varfields| sed 's/ /,/g'
# first add to header, cut from f2 to remove join-key pep seq field
head -n1 peps$count | cut -f echo $varfields | cut -f 2-5000| sed "s/^(\w)/${setn}\1/;s/(\s)/\1${setn}/g" > varhead
paste fixheader varhead > newheader && mv newheader fixheader
# then join the values
tail -n+2 peps$count | cut -f echo $varfields | sort -k1b,1 > sortpep; join peptable sortpep -a1 -a2 -o auto -e 'NA' -t $'\t' > joined
mv joined peptable
((count++))
done
join fixpeps peptable -a1 -a2 -o auto -e 'NA' -t $'\t' > fixvarpeps
executor > local (40)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[d2/52b362] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[51/98cbbc] process > concatFasta (1) [100%] 1 of 1 ✔
[97/1e08f0] process > makeProtSeq [100%] 1 of 1 ✔
[88/6a32b9] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[61/bb6b13] process > createSpectraLookup [100%] 1 of 1 ✔
[ac/ea0bc5] process > msgfPlus (3) [100%] 4 of 4 ✔
[f7/072e3c] process > percolator (1) [100%] 1 of 1 ✔
[1a/efdf28] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[c3/6d3c65] process > getNovelPercolator (1) [100%] 1 of 1 ✔
[1b/9b48b3] process > filterPercolator (1) [100%] 2 of 2 ✔
[84/66b904] process > svmToTSV (2) [100%] 2 of 2 ✔
[ff/db734c] process > createPSMTables (2) [100%] 2 of 2 ✔
[ae/5f8601] process > mergeSetPSMtable (1) [100%] 2 of 2 ✔
[23/f7f7df] process > prePeptideTable (2) [100%] 2 of 2 ✔
[30/3fec5d] process > createFastaBedGFF (1) [100%] 1 of 1 ✔
[60/299c1a] process > BlastPNovel (1) [100%] 1 of 1 ✔
[3d/fdfdb5] process > ParseBlastpOut (1) [100%] 1 of 1 ✔
[80/455017] process > ValidateSingleMismatchNovpeps (1) [100%] 1 of 1 ✔
[d3/75c83e] process > novpepSpecAIOutParse (1) [100%] 1 of 1 ✔
[af/63688c] process > BLATNovel (1) [100%] 1 of 1 ✔
[21/048bfb] process > parseBLATout (1) [100%] 1 of 1 ✔
[f9/4f1ee6] process > labelnsSNP (1) [100%] 1 of 1 ✔
[f8/7770a6] process > phastcons (1) [100%] 1 of 1 ✔
[ce/880aaa] process > phyloCSF (1) [100%] 1 of 1 ✔
[- ] process > scanBams -
[66/026dad] process > annovar (1) [100%] 1 of 1 ✔
[d1/944bac] process > parseAnnovarOut (1) [100%] 1 of 1 ✔
[4c/5230be] process > combineResults (1) [100%] 1 of 1 ✔
[f8/61a7ff] process > prepSpectrumAI (1) [100%] 1 of 1 ✔
[d1/b95be3] process > SpectrumAI (1) [100%] 1 of 1 ✔
[54/a5a93e] process > mapVariantPeptidesToGenome (1) [100%] 1 of 1 ✔
[a3/2fbf40] process > mergeSetPeptidetable (1) [100%] 2 of 2, failed: 1 ✘
WARN: Input tuple does not match input set cardinality declared by process combineResults -- offending value: [NA, /home/tana1/workspace/workflow13/work/f9/4f1ee6d02958ecde7615471292f5f3/nssnp.txt, /home/tana1/workspace/workflow13/work/d3/75c83e3c86c72fa583b9845477da55/novpep_specai.txt, /home/tana1/workspace/workflow13/work/21/048bfb80a397530b8ac253672cda6d/peptable_blat.txt, /home/tana1/workspace/workflow13/work/d1/944bac9c54df77706702fba00275ea/parsed_annovar.txt, /home/tana1/workspace/workflow13/work/f8/7770a6ad76319e6240704f100a5e2f/phastcons.txt, /home/tana1/workspace/workflow13/work/ce/880aaaf707413e3e154a788f2542cb/phylocsf.txt, /home/tana1/workspace/workflow13/work/30/3fec5d0e9a85149ee9b56ac64aff02/novpep_perco_quant.txt]
Error executing process > 'mergeSetPeptidetable (1)'

Caused by:
Process mergeSetPeptidetable (1) terminated with an error exit status (1)

Command executed:

build non-changing fields (seq based fields) table:

fixfields=head -n1 peps1 |tr -s '\t' '\n' | egrep -vn '(Setname|Spectrum|q-val|plex|Bare peptide)' | cut -f 1 -d ':'
fixfields=echo $fixfields | sed 's/ /,/g'
head -n1 peps1 | cut -f echo $fixfields > fixheader
count=1; for setn in NA ; do
cut -f echo $fixfields peps$count | tail -n+2 >> fixpeps
((count++))
done
if [ nov == 'nov' ]
then
cat fixheader <(sort -u -k1b,1 fixpeps) > temp
group_novpepToLoci.py --input temp --output temp.loci --distance 10kb
head -n1 temp.loci > fixheader
tail -n+2 temp.loci > fixpeps
fi
sort -u -k1b,1 fixpeps > temp
mv temp fixpeps

Build changing fields table

touch peptable
count=1; for setn in NA; do
varfields=head -n1 peps$count |tr -s '\t' '\n' | egrep -n '(Peptide|Spectrum|q-val|plex)' | cut -f 1 -d ':'
varfields=echo $varfields| sed 's/ /,/g'
# first add to header, cut from f2 to remove join-key pep seq field
head -n1 peps$count | cut -f echo $varfields | cut -f 2-5000| sed "s/^(\w)/${setn}\1/;s/(\s)/\1${setn}/g" > varhead
paste fixheader varhead > newheader && mv newheader fixheader
# then join the values
tail -n+2 peps$count | cut -f echo $varfields | sort -k1b,1 > sortpep; join peptable sortpep -a1 -a2 -o auto -e 'NA' -t $'\t' > joined
mv joined peptable
((count++))
done
join fixpeps peptable -a1 -a2 -o auto -e 'NA' -t $'\t' > fixvarpeps
cat fixheader fixvarpeps > nov_peptidetable.txt

Command exit status:
1

Command output:
(empty)

Command error:
Traceback (most recent call last):
File "/home/tana1/workspace/workflow13/bin/group_novpepToLoci.py", line 52, in
peplist.sort(key=lambda x:list(map(int,(x.chr,x.start))))
File "/home/tana1/workspace/workflow13/bin/group_novpepToLoci.py", line 52, in
peplist.sort(key=lambda x:list(map(int,(x.chr,x.start))))
ValueError: invalid literal for int() with base 10: 'NA'

Work dir:
/home/tana1/workspace/workflow13/work/a3/2fbf403f4fd60393ef6d0648d55a14

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
@TnakaNY
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TnakaNY commented Jan 8, 2020

Dear glormph:
Do you have any idea for this error?

@glormph
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glormph commented Jan 9, 2020

Hi, I am sorry, the holidays intervened. So I'm not sure what is wrong, the error seems to indicate that there is an entry given to group_novpepToLoci.py where there is NA instead of a chromosome and start position. If I'm not mistaken these entries would be calculated by the map_novelpeptide2genome.py script. So for some reason this must have not worked, and I think that the NA could be inserted by a bash join step, since the script itself doesnt seem to do that.

It's a bit hard to remotely troubleshoot, but I cant see anything you've done wrong. It could be that there are not enough peptides found. In that directory /home/tana1/workspace/workflow13/work/a3/2fbf403f4fd60393ef6d0648d55a14 there should be the file temp which is the (temporary) input to the script that crashes, and it should be some sort of peptide table. Does it look at all strange?

Maybe @yafeng has an idea about this (although he doesnt work here anymore).

@TnakaNY
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TnakaNY commented Jan 10, 2020

Hi glormph,
Thanks for reply.
I checked "temp" and it seemed not strange. I attached file here. Could you check it?
temp.txt

Also, i will try to run different raw files from LUMOS.

Thx.

@TnakaNY
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TnakaNY commented Jan 10, 2020

Hi glormph,
To make it sure that raw data itself is fine, could you tell me some publicly available label-free data that works well without error in your environment?
Using it, i can find where the problem is....

@glormph
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glormph commented Jan 29, 2020

Hi! First, we have never used the pipeline for anything other than TMT data yet, so I'm not sure which LF data would be best.

I looked at your file, and I think there is one peptide GTIYTSRELGWGKCRELFRWK, which does not get a chromosome position assigned in pipeline step createFastaBedGFF. This is possibly a problem with our pipeline, I havent been able to figure out where this goes wrong. You could possibly check what happens in the createFastaBedGFF process by looking in its .command.out or .command.err files and the in/output there, but I would have to do some more digging. As said before, I dont think you are doing anything wrong.

Changing the data would possibly work, since then you'll have other peptides, but that wouldn't solve this problem.

@TnakaNY
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TnakaNY commented Feb 6, 2020

Thank you! I will test again with TMT files from CPTAC dataset. When finished, will let you know.

@TnakaNY
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TnakaNY commented Mar 24, 2020

Hi,

I tried to analyze a proteome mzml file with TMT10-plex but got error below.
Proteome data was downloaded from here:
https://cptac-data-portal.georgetown.edu/study-summary/S038
Used file name is:
01CPTAC_OVprospective_W_PNNL_20161212_B1S1_f01.mzML

Fasta file: Uniprot 2018.Sep

Error message in console:
Error executing process > 'percolator (1)'

Caused by:
Process percolator (1) terminated with an error exit status (1)

Command executed:

echo [OVf01]
mkdir mzids
count=1;for sam in OVf01; do ln -s pwd/mzid$count mzids/${sam}.mzid; echo mzids/${sam}.mzid >> metafile; ((count++));done
msgf2pin -o percoin.xml -e trypsin -P "decoy_" metafile
percolator -j percoin.xml -X perco.xml -N 500000 --decoy-xml-output -y

Command exit status:
1

Command output:
[OVf01]

Command error:

Pin-converter version 3.01, Build Date Feb 5 2018 09:47:00
Copyright (c) 2013 Lukas Käll. All rights reserved.
Written by Lukas Käll (lukas.kall@scilifelab.se) in the
School of Biotechnology at KTH - Royal Institute of Technology, Stockholm.
Issued command:
msgf2pin -o percoin.xml -e trypsin -P decoy_ metafile
on 76c6e6a7caf5
Uses features for fragment spectra mass errors
Found a meta file: metafile
Reading mzids/OVf01.mzid
Error : parsing PSM: SII_27682_1
The error was: Error: current implementation can only handle UNIMOD accessions MS:1001460

Have you met same error when you analyzed TMT files?
I checked Percolator Github page and found one related issue.
percolator/percolator#89

Is it possible to fix by myself?

@higsch
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higsch commented Mar 24, 2020

Hi,
can you please share your modifications file? I have recently got a similar error due to the wrong usage of a UNIMOD accession.

@TnakaNY
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TnakaNY commented Mar 25, 2020

Hi,
Here is my mod file.
MSGFPlus_Mods_TMT10plex.txt

@higsch
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higsch commented Mar 25, 2020

I think you have to change TMT10plex to TMT6plex as this is the official UNIMOD identifier for this modification.
See also here: http://www.unimod.org/modifications_list.php?a=search&value=1&SearchFor=tmt&SearchOption=Contains&SearchField=

@TnakaNY
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TnakaNY commented Mar 27, 2020

Thank you!
I changed mod.file and tried it. It worked, but i got next error below....
I am now doubting "denomis".
The specification below is correct? I could not find setname information in downloaded mzml file.

$ sudo nextflow run main.nf --tdb /home/tana1/workspace/varDB/VarDB.fasta --mzmls /home/tana1/workspace/data/test4/*.mzML --activation hcd --isobaric tmt10plex --denoms 'set01:131' --gtf /home/tana1/workspace/varDB/VarDB.gtf --mods /home/tana1/workspace/mods/MSGFPlus_Mods_TMT6_10plex.txt --knownproteins /home/tana1/workspace/ensembl/Homo_sapiens.GRCh38.pep.all.fa --blastdb /home/tana1/workspace/varDB/UniProteome+Ensembl87+refseq+GENCODE24.proteins.fasta --cosmic /home/tana1/workspace/cosmic/CosmicMutantExport.tsv --snpfa /home/tana1/workspace/varDB/MSCanProVar_ensemblV79.filtered.fasta --genome /home/tana1/workspace/hg19/hg19.chr1-22.X.Y.M.fa.masked --dbsnp /home/tana1/workspace/varDB/snp151CodingDbSnp.txt --annovar_dir /home/tana1/workspace/annovar/annovar --bigwigs /home/tana1/workspace/bigwig --outdir /home/tana1/workspace/result19_2 -profile docker,standard
[sudo] password for tana1:
N E X T F L O W ~ version 19.10.0
Launching main.nf [fervent_dubinsky] - revision: 6ff5d47fa2
1 mzML files in analysis
Detected setnames: NA
[- ] process > splitSetNormalSearchPsms -
executor > local (4)
executor > local (4)
[- ] process > splitSetNormalSearchPsms -
executor > local (4)
[- ] process > splitSetNormalSearchPsms -
executor > local (5)
[- ] process > splitSetNormalSearchPsms -
executor > local (5)
executor > local (15)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[ef/f3a546] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[52/312323] process > concatFasta (1) [100%] 1 of 1 ✔
[4c/28e59c] process > makeProtSeq [100%] 1 of 1 ✔
[c3/c7ed88] process > makeTrypSeq [100%] 1 of 1 ✔
[c5/636fda] process > IsobaricQuant (1) [100%] 1 of 1 ✔
[46/26ac4b] process > createSpectraLookup [100%] 1 of 1 ✔
[a7/f860e9] process > msgfPlus (1) [100%] 1 of 1 ✔
[73/fb98a6] process > percolator (1) [100%] 1 of 1 ✔
[57/7df96c] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[27/3081a5] process > getNovelPercolator (1) [100%] 1 of 1 ✔
[f5/336f5c] process > filterPercolator (1) [100%] 2 of 2 ✔
[a5/28456b] process > svmToTSV (1) [ 50%] 1 of 2
[9c/1f3fd3] process > createPSMTables (1) [100%] 1 of 1
[- ] process > mergeSetPSMtable -
executor > local (15)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[ef/f3a546] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[52/312323] process > concatFasta (1) [100%] 1 of 1 ✔
[4c/28e59c] process > makeProtSeq [100%] 1 of 1 ✔
[c3/c7ed88] process > makeTrypSeq [100%] 1 of 1 ✔
[c5/636fda] process > IsobaricQuant (1) [100%] 1 of 1 ✔
[46/26ac4b] process > createSpectraLookup [100%] 1 of 1 ✔
[a7/f860e9] process > msgfPlus (1) [100%] 1 of 1 ✔
[73/fb98a6] process > percolator (1) [100%] 1 of 1 ✔
[57/7df96c] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[27/3081a5] process > getNovelPercolator (1) [100%] 1 of 1 ✔
[f5/336f5c] process > filterPercolator (1) [100%] 2 of 2 ✔
[d7/b55f7b] process > svmToTSV (2) [100%] 2 of 2, failed: 1
[9c/1f3fd3] process > createPSMTables (1) [100%] 1 of 1
[- ] process > mergeSetPSMtable -
[- ] process > prePeptideTable -
[- ] process > createFastaBedGFF -
[- ] process > BlastPNovel -
[- ] process > ParseBlastpOut -
[- ] process > ValidateSingleMismatchNovpeps -
[- ] process > novpepSpecAIOutParse -
[- ] process > BLATNovel -
[- ] process > parseBLATout -
[- ] process > labelnsSNP -
[- ] process > phastcons -
[- ] process > phyloCSF -
[- ] process > scanBams -
[- ] process > annovar -
[- ] process > parseAnnovarOut -
[- ] process > combineResults -
[- ] process > prepSpectrumAI -
[- ] process > SpectrumAI -
[- ] process > mapVariantPeptidesToGenome -
[- ] process > mergeSetPeptidetable -
WARN: Killing pending tasks (1)
Error executing process > 'prePeptideTable (1)'

Caused by:
Cannot invoke method join() on null object

Source block:
"""
msspeptable psm2pep -i psms.txt -o preisoquant --scorecolpattern svm --spectracol 1 ${params.isobaric ? '--isobquantcolpattern plex' : ''}
awk -F '\t' 'BEGIN {OFS = FS} {print $13,$14,$3,$8,$9,$10,$12,$15,$16,$17,$18,$19,$20,$21,$22,$23}' preisoquant > preordered
${params.isobaric ? "msspsmtable isoratio -i psms.txt -o peptidetable.txt --targettable preordered --isobquantcolpattern plex --minint 0.1 --denompatterns ${set_denoms.value[setname].join(' ')} --protcol 12" : 'mv preordered peptidetable.txt'}
"""

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

@TnakaNY
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TnakaNY commented Mar 27, 2020

I have additional questions;

For latest pipeline, can i use latest version of CosmicMutantExport.tsv?
Should I use older version such as grch37/cosmic/v81/? (v81 is not currently available).

Then, how about SNP?
Should I also use "snp142CodingDbSnp.txt(hg19)" instead of latest version

@yafeng
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yafeng commented Mar 28, 2020

these two files are used to find chromosome coordinates for detected SNPs or mutations.
if you want to understand how it works, the corresponding script is under bin folder "map_cosmic_snp_tohg19.py".

The key to match between the peptide and entries in the databases are contained in the Fasta header of variant peptides in VarDB database, which I suggest you to take a look as well (the header of variant peptides start with "CanProVar" and "COSMIC").
As long as the latest version contains the columns to match the key, it should work.

@TnakaNY
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TnakaNY commented Mar 28, 2020

Hi Yafeng,

Thank you for comment,

I just wanted to make same environment as yours including database files because it is easy to find where the error is.

Which version of CosmicMutantExport (v81 or v85 or v91) and SNP (142 or 151 or latest) do you use for latest version(17 Dec 2019) in your enveronment?

@TnakaNY
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TnakaNY commented Apr 10, 2020

I recurrently got a error below. It seemed to be related "--denoms" parameter.
It seemed the program did not recognize denoms name as shown "detected setname:NA"

I could not find how to set denoms paramer. How can I set denoms name?

The data is TMT 10plex-labled data from QE from CPTAC.
9 clinical tumor samples and internal control (total 10, 126 label was used for control) were labeled. Then, all samples were mixed up and fractionated into 24.
So , the MS dataset has 24 mzml files. To test pipeline shortly, I used only one file.

Could anyone help me?

Used command and console error are here:
$ sudo nextflow run main.nf --tdb /home/tana1/workspace/varDB/VarDB.fasta --mzmls /home/tana1/workspace/data/test4/*.mzML --activation hcd --isobaric tmt10plex --denoms 'set01:131' --gtf /home/tana1/workspace/varDB/VarDB.gtf --mods /home/tana1/workspace/mods/MSGFPlus_Mods_TMT6_10plex.txt --knownproteins /home/tana1/workspace/ensembl/Homo_sapiens.GRCh38.pep.all.fa --blastdb /home/tana1/workspace/varDB/UniProteome+Ensembl87+refseq+GENCODE24.proteins.fasta --cosmic /home/tana1/workspace/cosmic/CosmicMutantExport.tsv --snpfa /home/tana1/workspace/varDB/MSCanProVar_ensemblV79.filtered.fasta --genome /home/tana1/workspace/hg19/hg19.chr1-22.X.Y.M.fa --dbsnp /home/tana1/workspace/varDB/snp151CodingDbSnp.txt --annovar_dir /home/tana1/workspace/annovar/annovar --bigwigs /home/tana1/workspace/bigwig --outdir /home/tana1/workspace/result19_2 -profile docker,standard
[sudo] password for tana1:
N E X T F L O W ~ version 19.10.0
Launching main.nf [fervent_dubinsky] - revision: 6ff5d47fa2
1 mzML files in analysis
Detected setnames: NA

Error:
WARN: Killing pending tasks (1)
Error executing process > 'prePeptideTable (1)'

Caused by:
Cannot invoke method join() on null object

Source block:
"""
msspeptable psm2pep -i psms.txt -o preisoquant --scorecolpattern svm --spectracol 1 ${params.isobaric ? '--isobquantcolpattern plex' : ''}
awk -F '\t' 'BEGIN {OFS = FS} {print $13,$14,$3,$8,$9,$10,$12,$15,$16,$17,$18,$19,$20,$21,$22,$23}' preisoquant > preordered
${params.isobaric ? "msspsmtable isoratio -i psms.txt -o peptidetable.txt --targettable preordered --isobquantcolpattern plex --minint 0.1 --denompatterns ${set_denoms.value[setname].join(' ')} --protcol 12" : 'mv preordered peptidetable.txt'}
"""

@TnakaNY
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TnakaNY commented Apr 16, 2020

Hi Glormph,
Do you have any idea for this error?
I could not understand requirements for --denoms parameter, completely.

@glormph
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glormph commented Apr 29, 2020 •
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Hi, and sorry for not replying earlier. So the --denoms parameter specifies which denominators the isobaric (TMT, iTRAQ) quantification uses. You've specified this correctly, but the pipeline does not know that the set01 part exists since the spectra files are not defined with a sample set. If you want to run multiple sample sets you probably want to specify your files in a definition text file, containing one line per file / set which are tab separated:

/path/to/file\tsetname

Otherwise you could specify --denoms "NA:131" to use the fallback NA setname.

@TnakaNY
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TnakaNY commented Apr 29, 2020

Thank you! Please let me try it.

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@glormph @yafeng @higsch @TnakaNY