Closed TnakaNY closed 4 years ago
Used command line is here: nextflow run main.nf --tdb /home/tana1/proteogenomics-analysis/lehtiolab-clone/varDB/VarDB.fasta --mzmldef /home/tana1/proteogenomics-analysis/lehtiolab-clone/data/test1/Test.mzML --activation hcd --gtf /home/tana1/proteogenomics-analysis/lehtiolab-clone/varDB/VarDB.gtf --mods /home/tana1/proteogenomics-analysis/lehtiolab-clone/MSFGPlus_Mods_FFPEv1.txt --knownproteins /home/tana1/proteogenomics-analysis/lehtiolab-clone/ensembl/Homo_sapiens.GRCh38.pep.all.fa --blastdb /home/tana1/proteogenomics-analysis/lehtiolab-clone/varDB/UniProteome+Ensembl87+GENCODE24.proteins.fasta --cosmic /home/tana1/proteogenomics-analysis/lehtiolab-clone/cosmic/CosmicMutantExport.tsv --snpfa /home/tana1/proteogenomics-analysis/lehtiolab-clone/varDB/MSCanProVar_ensemblV79.filtered.fasta --genome /home/tana1/proteogenomics-analysis/lehtiolab-clone/hg19/hg19.chr1-22.X.Y.M.fa.masked --dbsnp /home/tana1/proteogenomics-analysis/lehtiolab-clone/varDB/snp151CodingDbSnp.txt --annovar_dir /home/tana1/proteogenomics-analysis/lehtiolab-clone/annovar/annovar --bigwigs /home/tana1/proteogenomics-analysis/lehtiolab-clone/bigwig --outdir /home/tana1/proteogenomics-analysis/lehtiolab-clone/result -profile testing
Hi, I am not sure about the errors but they both have something to do with the mzML input file. I can see one problem in your command, you have:
--mzmldef /path/to/file.mzML
That option expects a text file with paths to mzML files (I am asssuming that you passed an mzML file). You can either:
--mzmls "/path/to/file.mzML"
or create a TSV text file to give to --mzmldef
, which contains the path to an mzML file on each row (and tab-separated, the name of the sample (set) ).
Thank you! "mzmls" solved error1. But i had another error in making docker container (HTTP000 error in container preparing; cannot access to repository from the container). Maybe, I will ask you guys again for help.
Best, Tana
HI, I solved docker internet access problem by changing OS from CentOS8 to Ubuntu18.04. I could successfully build docker container. But, I faced other errors below.
My system: Physical PC OS: windows 10 Pro Virtualbox OS: Ubuntu18.04 with docker ce
i ran below command from Ubuntu terminal (from a directory with "main.nf" file): sudo nextflow run main.nf --tdb /home/tana1/workspace/varDB/VarDB.fasta --mzmls /home/tana1/workspace/data/test1/Test.mzML --activation hcd --gtf /home/tana1/workspace/varDB/VarDB.gtf --mods /home/tana1/workspace/mods/MSFGPlus_Mods_FFPEv1.txt --knownproteins /home/tana1/workspace/ensembl/Homo_sapiens.GRCh38.pep.all.fa --blastdb /home/tana1/workspace/varDB/UniProteome+Ensembl87+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/result -profile testing
Then, I got this error in my terminal:
(base) tana1@tana1-VirtualBox:~/workspace/workflow1$ nextflow run main.nf --tdb /home/tana1/workspace/varDB/VarDB.fasta --mzmls /home/tana1/workspace/data/test1/Test.mzML --activation hcd --gtf /home/tana1/workspace/varDB/VarDB.gtf --mods /home/tana1/workspace/mods/MSFGPlus_Mods_FFPEv1.txt --knownproteins /home/tana1/workspace/ensembl/Homo_sapiens.GRCh38.pep.all.fa --blastdb /home/tana1/workspace/varDB/UniProteome+Ensembl87+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/result -profile testing
N E X T F L O W ~ version 19.10.0
Launching main.nf
[golden_hodgkin] - revision: 0194305a29
1 mzML files in analysis
Detected setnames: NA
[- ] process > splitSetNormalSearchPsms -
executor > local (4)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[ca/7a5b2c] process > makeTargetSeqLookup (1) [ 0%] 0 of 1
[- ] process > concatFasta -
[e8/9d0200] process > makeProtSeq [ 0%] 0 of 1
[52/011097] process > makeTrypSeq [ 0%] 0 of 1
[- ] process > IsobaricQuant -
[47/15cf4b] process > createSpectraLookup [ 0%] 0 of 1
[- ] process > msgfPlus -
[- ] process > percolator -
executor > local (4)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[ca/7a5b2c] process > makeTargetSeqLookup (1) [ 0%] 0 of 1
[- ] process > concatFasta -
[e8/9d0200] process > makeProtSeq [ 0%] 0 of 1
[52/011097] process > makeTrypSeq [ 0%] 0 of 1
[- ] process > IsobaricQuant -
[47/15cf4b] process > createSpectraLookup [ 0%] 0 of 1
[- ] process > msgfPlus -
[- ] process > percolator -
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
[- ] process > filterPercolator -
[- ] process > svmToTSV -
[- ] process > createPSMTables -
[- ] 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 -
WARN: Input tuple does not match input set cardinality declared by process splitSetNormalSearchPsms
-- offending value: NA
Error executing process > 'makeProtSeq'
executor > local (4)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[ca/7a5b2c] process > makeTargetSeqLookup (1) [100%] 1 of 1, failed: 1
[- ] process > concatFasta -
[e8/9d0200] process > makeProtSeq [100%] 1 of 1, failed: 1 ✘
[52/011097] process > makeTrypSeq [100%] 1 of 1, failed: 1 ✘
[- ] process > IsobaricQuant -
[47/15cf4b] process > createSpectraLookup [100%] 1 of 1, failed: 1
[- ] process > msgfPlus -
[- ] process > percolator -
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
[- ] process > filterPercolator -
[- ] process > svmToTSV -
[- ] process > createPSMTables -
[- ] 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: Input tuple does not match input set cardinality declared by process splitSetNormalSearchPsms
-- offending value: NA
WARN: Killing pending tasks (2)
Error executing process > 'makeProtSeq'
Caused by:
Process makeProtSeq
terminated with an error exit status (127)
Command executed:
msslookup protspace -i Homo_sapiens.GRCh38.pep.all.fa --minlen 8
Command exit status: 127
Command output: (empty)
Command error: .command.sh: line 2: msslookup: command not found
Work dir: /home/tana1/workspace/workflow1/work/e8/9d0200ec80d29bea926d89e0ea6fda
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
I could not find/understand what is wrong. I am a completely beginner for docker, nextflow, and Linux OS. Should I start docker container ($ sudo docker run nfcore/base) before starting main.nf? Or should i run the nextflow command from the container (probably not, i guess)?
Best, Tana
Even though i started the container, i received same errors (above).
I think you almost had it right, nextflow will pull the docker container for you. The parameter -profile testing
should probably be -profile docker,standard
. Without that it will not run docker.
Also -resume
is good to add so you can in the future rerun without rerunning any already-completed tasks.
Thank you. Using "-profile docker,standard", it ran successfully. But, i still some errors below.
(base) tana1@tana1-VirtualBox:~/workspace/workflow3$ sudo nextflow run main.nf --tdb /home/tana1/workspace/varDB/VarDB.fasta --mzmls /home/tana1/workspace/data/test1/Test.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/result3 -profile docker,standard
[sudo] password for tana1:
N E X T F L O W ~ version 19.10.0
Launching main.nf
[thirsty_pauling] - revision: 0194305a29
1 mzML files in analysis
Detected setnames: NA
[- ] process > splitSetNormalSearchPsms -
executor > local (3)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [ 0%] 0 of 1
[- ] process > concatFasta -
[76/577871] process > makeProtSeq [ 0%] 0 of 1
[32/8eb1de] 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 -
[36/08f8e7] process > makeTargetSeqLookup (1) [ 0%] 0 of 1
[- ] process > concatFasta -
[76/577871] process > makeProtSeq [ 0%] 0 of 1
[32/8eb1de] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[e6/747314] 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 -
[36/08f8e7] process > makeTargetSeqLookup (1) [ 0%] 0 of 1
[- ] process > concatFasta -
[76/577871] process > makeProtSeq [ 0%] 0 of 1
[32/8eb1de] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[e6/747314] process > createSpectraLookup [100%] 1 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 -
[36/08f8e7] process > makeTargetSeqLookup (1) [ 0%] 0 of 1
[- ] process > concatFasta -
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
[32/8eb1de] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[e6/747314] process > createSpectraLookup [100%] 1 of 1 ✔
[- ] process > msgfPlus -
[- ] process > percolator -
[- ] process > getVariantPercolator -
[- ] process > getNovelPercolator -
[- ] process > filterPercolator -
executor > local (5)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [ 0%] 0 of 1
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (6)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (7)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (8)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (9)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (9)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (11)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (12)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (13)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (14)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (16)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (17)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (17)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (18)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (20)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
[32/8eb1de] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
executor > local (21)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (21)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (22)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
[32/8eb1de] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
executor > local (23)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (25)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (26)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (27)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (28)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (29)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (30)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (31)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (32)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (33)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (33)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (34)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (34)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
executor > local (35)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
[32/8eb1de] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[e6/747314] process > createSpectraLookup [100%] 1 of 1 ✔
[86/e7a85e] process > msgfPlus (1) [100%] 1 of 1 ✔
[44/4c0d36] process > percolator (1) [100%] 1 of 1 ✔
[b1/e18bb8] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[16/6fd7e5] process > getNovelPercolator (1) [100%] 1 of 1 ✔
[7b/fe5628] process > filterPercolator (1) [100%] 2 of 2 ✔
[d5/dc13c4] process > svmToTSV (2) [100%] 2 of 2 ✔
[f2/252ac5] process > createPSMTables (2) [100%] 2 of 2 ✔
executor > local (37)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
[32/8eb1de] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[e6/747314] process > createSpectraLookup [100%] 1 of 1 ✔
[86/e7a85e] process > msgfPlus (1) [100%] 1 of 1 ✔
[44/4c0d36] process > percolator (1) [100%] 1 of 1 ✔
[b1/e18bb8] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[16/6fd7e5] process > getNovelPercolator (1) [100%] 1 of 1 ✔
[7b/fe5628] process > filterPercolator (1) [100%] 2 of 2 ✔
[d5/dc13c4] process > svmToTSV (2) [100%] 2 of 2 ✔
[f2/252ac5] process > createPSMTables (2) [100%] 2 of 2 ✔
[d4/e5f257] process > mergeSetPSMtable (2) [100%] 2 of 2 ✔
[19/52bee5] process > prePeptideTable (2) [100%] 2 of 2 ✔
[94/657c9c] process > createFastaBedGFF (1) [100%] 1 of 1 ✔
[90/6fc520] process > BlastPNovel (1) [100%] 1 of 1 ✔
executor > local (37)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[36/08f8e7] process > makeTargetSeqLookup (1) [100%] 1 of 1 ✔
[c6/da5e07] process > concatFasta (1) [100%] 1 of 1 ✔
[76/577871] process > makeProtSeq [100%] 1 of 1 ✔
[32/8eb1de] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[e6/747314] process > createSpectraLookup [100%] 1 of 1 ✔
[86/e7a85e] process > msgfPlus (1) [100%] 1 of 1 ✔
[44/4c0d36] process > percolator (1) [100%] 1 of 1 ✔
[b1/e18bb8] process > getVariantPercolator (1) [100%] 1 of 1 ✔
[16/6fd7e5] process > getNovelPercolator (1) [100%] 1 of 1 ✔
[7b/fe5628] process > filterPercolator (1) [100%] 2 of 2 ✔
[d5/dc13c4] process > svmToTSV (2) [100%] 2 of 2 ✔
[f2/252ac5] process > createPSMTables (2) [100%] 2 of 2 ✔
[d4/e5f257] process > mergeSetPSMtable (2) [100%] 2 of 2 ✔
[19/52bee5] process > prePeptideTable (2) [100%] 2 of 2 ✔
[94/657c9c] process > createFastaBedGFF (1) [100%] 1 of 1 ✔
[90/6fc520] process > BlastPNovel (1) [100%] 1 of 1 ✔
[44/00bba3] process > ParseBlastpOut (1) [100%] 1 of 1 ✔
[92/d4b9c1] process > ValidateSingleMismatchNovpe... [100%] 1 of 1 ✔
[1d/8ea14b] process > novpepSpecAIOutParse (1) [100%] 1 of 1 ✔
[9f/9a383b] process > BLATNovel (1) [100%] 1 of 1 ✔
[49/776b03] process > parseBLATout (1) [100%] 1 of 1 ✔
[3f/7fd623] process > labelnsSNP (1) [100%] 1 of 1 ✔
[a3/02523a] process > phastcons (1) [100%] 1 of 1 ✔
[3b/0f8079] process > phyloCSF (1) [100%] 1 of 1 ✔
[- ] process > scanBams -
[0f/839daf] process > annovar (1) [100%] 1 of 1 ✔
[cf/d4efca] process > parseAnnovarOut (1) [100%] 1 of 1 ✔
[6b/0f9dd3] process > combineResults (1) [100%] 1 of 1 ✔
[86/1d0f35] process > prepSpectrumAI (1) [100%] 1 of 1 ✔
[a7/1cbcaf] process > SpectrumAI (1) [100%] 1 of 1 ✔
[4b/9fdd04] process > mapVariantPeptidesToGenome (1) [100%] 1 of 1 ✔
[f1/2c478d] process > mergeSetPeptidetable (1) [100%] 2 of 2 ✔
WARN: Input tuple does not match input set cardinality declared by process combineResults
-- offending value: [NA, /home/tana1/workspace/workflow3/work/3f/7fd623f92cd9c77733e05d3dea2e95/nssnp.txt, /home/tana1/workspace/workflow3/work/1d/8ea14b6b247a588da54f5d7e7bbfb6/novpep_specai.txt, /home/tana1/workspace/workflow3/work/49/776b03a7f264d6599506a46eda14be/peptable_blat.txt, /home/tana1/workspace/workflow3/work/cf/d4efca5cdb788dc8b158690901814a/parsed_annovar.txt, /home/tana1/workspace/workflow3/work/a3/02523aca32bedc630056a3bf2d87be/phastcons.txt, /home/tana1/workspace/workflow3/work/3b/0f8079e4d7574412b8035eae48e9da/phylocsf.txt, /home/tana1/workspace/workflow3/work/94/657c9c641da0bc34f5da5d99af31a5/novpep_perco_quant.txt]
Completed at: 13-Dec-2019 12:20:55
Duration : 2h 19m 37s
CPU hours : 7.8
Succeeded : 37
And, i saw this error message while the program running. WARN: Input tuple does not match input set cardinality declared by process 'splitSetNormalSearchPsm' -- offending value: NA
Could you tell me how to solve this error?
Best, Tana
They are "only" warnings and not errors, so you can safely ignore them. They would disappear with different settings but that is in this case dependent on input data. So you're fine :)
Thank you for quick reply. According to terminal, it seemed that some processes were not done. But, it does not matter, right?
[- ] process > splitSetNormalSearchPsms - [- ] process > splitPlateNormalSearchPsms - [- ] process > normalSearchPsmsToPeptides - [- ] process > create6FTDB -
Exactly, those are run in other circumstances, when you prefractionate using isoelectric focusing.
Hi, I have another error. When i analyzed 1 or 2 mzml file, it worked well (above). But, using 4 mzml files, i failed to analyzed it. "MergeSetPeptidetable" step had error. Here attached is a copy of terminal. My virtual machine has 60GB RAM, 2GB swap memory, 32vCPU.
How can I solve this issue?
(base) tana1@tana1-VirtualBox:~/workspace/workflow5$ 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/result5 -profile docker,standard
[sudo] password for tana1:
N E X T F L O W ~ version 19.10.0
Launching main.nf
[magical_montalcini] - revision: 0194305a29
4 mzML files in analysis
Detected setnames: NA
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitSetNormalSearchPsms -
executor > local (3)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
executor > local (3)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLookup (1) [ 0%] 0 of 1
[- ] process > concatFasta -
[1b/ad9eae] process > makeProtSeq [ 0%] 0 of 1
[27/3bbffd] process > makeTrypSeq [ 0%] 0 of 1
[- ] process > IsobaricQuant -
[- ] process > createSpectraLookup -
[- ] process > msgfPlus -
[- ] process > percolator -
executor > local (3)
[- ] process > splitSetNormalSearchPsms -
[- ] process > splitPlateNormalSearchPsms -
[- ] process > normalSearchPsmsToPeptides -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLookup (1) [ 0%] 0 of 1
[- ] process > concatFasta -
[1b/ad9eae] process > makeProtSeq [ 0%] 0 of 1
[27/3bbffd] 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 -
[0c/a9e89d] process > makeTargetSeqLookup (1) [ 0%] 0 of 1
[- ] process > concatFasta -
[1b/ad9eae] process > makeProtSeq [ 0%] 0 of 1
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [ 0%] 0 of 1
[- ] process > msgfPlus -
[- ] process > percolator -
executor > local (4)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [ 0%] 0 of 1
[- ] process > concatFasta -
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [ 0%] 0 of 1
[- ] process > msgfPlus -
executor > local (4)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [ 0%] 0 of 1
[- ] process > concatFasta -
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (5)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [ 0%] 0 of 1
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (6)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (8)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (9)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (9)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (9)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (10)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (12)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (12)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (14)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (15)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (15)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (16)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (16)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (17)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (17)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (19)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (20)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (21)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (23)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
[28/a29d10] process > msgfPlus (2) [100%] 4 of 4 ✔
[68/358ee4] process > percolator (1) [100%] 1 of 1 ✔
executor > local (25)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
[28/a29d10] process > msgfPlus (2) [100%] 4 of 4 ✔
[68/358ee4] process > percolator (1) [100%] 1 of 1 ✔
executor > local (25)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (27)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (27)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (28)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (29)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (30)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (31)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (32)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (33)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (34)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (35)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (36)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (37)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (37)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (37)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
executor > local (38)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
[28/a29d10] process > msgfPlus (2) [100%] 4 of 4 ✔
[68/358ee4] process > percolator (1) [100%] 1 of 1 ✔
[b8/4b45a1] process > getVariantPercola... [100%] 1 of 1 ✔
[b1/505778] process > getNovelPercolato... [100%] 1 of 1 ✔
[9f/d6a382] process > filterPercolator (1) [100%] 2 of 2 ✔
[0f/76b8b8] process > svmToTSV (2) [100%] 2 of 2 ✔
[ee/d6a040] process > createPSMTables (2) [100%] 2 of 2 ✔
[6e/fc02dc] process > mergeSetPSMtable (1) [100%] 2 of 2 ✔
[c4/789790] process > prePeptideTable (2) [100%] 2 of 2 ✔
[4f/714a7d] process > createFastaBedGFF... [100%] 1 of 1 ✔
[a8/d8e934] process > BlastPNovel (1) [100%] 1 of 1 ✔
executor > local (40)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
[28/a29d10] process > msgfPlus (2) [100%] 4 of 4 ✔
[68/358ee4] process > percolator (1) [100%] 1 of 1 ✔
[b8/4b45a1] process > getVariantPercola... [100%] 1 of 1 ✔
[b1/505778] process > getNovelPercolato... [100%] 1 of 1 ✔
[9f/d6a382] process > filterPercolator (1) [100%] 2 of 2 ✔
[0f/76b8b8] process > svmToTSV (2) [100%] 2 of 2 ✔
[ee/d6a040] process > createPSMTables (2) [100%] 2 of 2 ✔
[6e/fc02dc] process > mergeSetPSMtable (1) [100%] 2 of 2 ✔
[c4/789790] process > prePeptideTable (2) [100%] 2 of 2 ✔
[4f/714a7d] process > createFastaBedGFF... [100%] 1 of 1 ✔
[a8/d8e934] process > BlastPNovel (1) [100%] 1 of 1 ✔
[8b/17bff6] process > ParseBlastpOut (1) [100%] 1 of 1 ✔
[9a/431a29] process > ValidateSingleMis... [100%] 1 of 1 ✔
executor > local (40)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
[28/a29d10] process > msgfPlus (2) [100%] 4 of 4 ✔
[68/358ee4] process > percolator (1) [100%] 1 of 1 ✔
[b8/4b45a1] process > getVariantPercola... [100%] 1 of 1 ✔
[b1/505778] process > getNovelPercolato... [100%] 1 of 1 ✔
[9f/d6a382] process > filterPercolator (1) [100%] 2 of 2 ✔
[0f/76b8b8] process > svmToTSV (2) [100%] 2 of 2 ✔
[ee/d6a040] process > createPSMTables (2) [100%] 2 of 2 ✔
[6e/fc02dc] process > mergeSetPSMtable (1) [100%] 2 of 2 ✔
[c4/789790] process > prePeptideTable (2) [100%] 2 of 2 ✔
[4f/714a7d] process > createFastaBedGFF... [100%] 1 of 1 ✔
[a8/d8e934] process > BlastPNovel (1) [100%] 1 of 1 ✔
executor > local (40)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
[28/a29d10] process > msgfPlus (2) [100%] 4 of 4 ✔
[68/358ee4] process > percolator (1) [100%] 1 of 1 ✔
[b8/4b45a1] process > getVariantPercola... [100%] 1 of 1 ✔
[b1/505778] process > getNovelPercolato... [100%] 1 of 1 ✔
[9f/d6a382] process > filterPercolator (1) [100%] 2 of 2 ✔
[0f/76b8b8] process > svmToTSV (2) [100%] 2 of 2 ✔
[ee/d6a040] process > createPSMTables (2) [100%] 2 of 2 ✔
[6e/fc02dc] process > mergeSetPSMtable (1) [100%] 2 of 2 ✔
[c4/789790] process > prePeptideTable (2) [100%] 2 of 2 ✔
[4f/714a7d] process > createFastaBedGFF... [100%] 1 of 1 ✔
[a8/d8e934] process > BlastPNovel (1) [100%] 1 of 1 ✔
[8b/17bff6] process > ParseBlastpOut (1) [100%] 1 of 1 ✔
[9a/431a29] process > ValidateSingleMis... [100%] 1 of 1 ✔
[76/a5cc23] process > novpepSpecAIOutPa... [100%] 1 of 1 ✔
[30/908585] process > BLATNovel (1) [100%] 1 of 1 ✔
[96/110651] process > parseBLATout (1) [100%] 1 of 1 ✔
[7a/26fde6] process > labelnsSNP (1) [100%] 1 of 1 ✔
[a8/08cbc8] process > phastcons (1) [100%] 1 of 1 ✔
[73/d5195d] process > phyloCSF (1) [100%] 1 of 1 ✔
[- ] process > scanBams -
[61/4c5675] process > annovar (1) [100%] 1 of 1 ✔
[a6/cefbdb] process > parseAnnovarOut (1) [100%] 1 of 1 ✔
[47/4aa3a2] process > combineResults (1) [100%] 1 of 1 ✔
[c8/e9a7c8] process > prepSpectrumAI (1) [100%] 1 of 1 ✔
[b6/fac0f2] process > SpectrumAI (1) [100%] 1 of 1 ✔
[c7/0384fd] process > mapVariantPeptide... [100%] 1 of 1 ✔
[38/e02d0d] process > mergeSetPeptideta... [ 50%] 1 of 2
WARN: Input tuple does not match input set cardinality declared by process combineResults
-- offending value: [NA, /home/tana1/workspace/workflow5/work/7a/26fde6671af89bdc83e882411ae741/nssnp.txt, /home/tana1/workspace/workflow5/work/76/a5cc23f6b4ae7dbe452cb5d7598d76/novpep_specai.txt, /home/tana1/workspace/workflow5/work/96/110651f7fdeeff426a88a68855814f/peptable_blat.txt, /home/tana1/workspace/workflow5/work/a6/cefbdb68afbfa3a1d42e82a10ab3d4/parsed_annovar.txt, /home/tana1/workspace/workflow5/work/a8/08cbc8ac3de91507e6e5f62accb5c7/phastcons.txt, /home/tana1/workspace/workflow5/work/73/d5195d4b929919c3ab0cd5799a2d2c/phylocsf.txt, /home/tana1/workspace/workflow5/work/4f/714a7d885220f77c9fa0cf5b4f744f/novpep_perco_quant.txt]
Error executing process > 'mergeSetPeptidetable (1)'
Caused by:
Process mergeSetPeptidetable (1)
terminated with an error exit status (1)
Command executed:
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
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 $varfields| sed 's/ /,/g'
head -n1 peps$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
executor > local (40)
[- ] process > splitSetNormalSea... -
[- ] process > splitPlateNormalS... -
[- ] process > normalSearchPsmsT... -
[- ] process > create6FTDB -
[0c/a9e89d] process > makeTargetSeqLook... [100%] 1 of 1 ✔
[f0/5aba81] process > concatFasta (1) [100%] 1 of 1 ✔
[1b/ad9eae] process > makeProtSeq [100%] 1 of 1 ✔
[27/3bbffd] process > makeTrypSeq [100%] 1 of 1 ✔
[- ] process > IsobaricQuant -
[4d/417c8d] process > createSpectraLookup [100%] 1 of 1 ✔
[28/a29d10] process > msgfPlus (2) [100%] 4 of 4 ✔
[68/358ee4] process > percolator (1) [100%] 1 of 1 ✔
[b8/4b45a1] process > getVariantPercola... [100%] 1 of 1 ✔
[b1/505778] process > getNovelPercolato... [100%] 1 of 1 ✔
[9f/d6a382] process > filterPercolator (1) [100%] 2 of 2 ✔
[0f/76b8b8] process > svmToTSV (2) [100%] 2 of 2 ✔
[ee/d6a040] process > createPSMTables (2) [100%] 2 of 2 ✔
[6e/fc02dc] process > mergeSetPSMtable (1) [100%] 2 of 2 ✔
[c4/789790] process > prePeptideTable (2) [100%] 2 of 2 ✔
[4f/714a7d] process > createFastaBedGFF... [100%] 1 of 1 ✔
[a8/d8e934] process > BlastPNovel (1) [100%] 1 of 1 ✔
[8b/17bff6] process > ParseBlastpOut (1) [100%] 1 of 1 ✔
[9a/431a29] process > ValidateSingleMis... [100%] 1 of 1 ✔
[76/a5cc23] process > novpepSpecAIOutPa... [100%] 1 of 1 ✔
[30/908585] process > BLATNovel (1) [100%] 1 of 1 ✔
[96/110651] process > parseBLATout (1) [100%] 1 of 1 ✔
[7a/26fde6] process > labelnsSNP (1) [100%] 1 of 1 ✔
[a8/08cbc8] process > phastcons (1) [100%] 1 of 1 ✔
[73/d5195d] process > phyloCSF (1) [100%] 1 of 1 ✔
[- ] process > scanBams -
[61/4c5675] process > annovar (1) [100%] 1 of 1 ✔
[a6/cefbdb] process > parseAnnovarOut (1) [100%] 1 of 1 ✔
[47/4aa3a2] process > combineResults (1) [100%] 1 of 1 ✔
[c8/e9a7c8] process > prepSpectrumAI (1) [100%] 1 of 1 ✔
[b6/fac0f2] process > SpectrumAI (1) [100%] 1 of 1 ✔
[c7/0384fd] process > mapVariantPeptide... [100%] 1 of 1 ✔
[28/515862] process > mergeSetPeptideta... [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/workflow5/work/7a/26fde6671af89bdc83e882411ae741/nssnp.txt, /home/tana1/workspace/workflow5/work/76/a5cc23f6b4ae7dbe452cb5d7598d76/novpep_specai.txt, /home/tana1/workspace/workflow5/work/96/110651f7fdeeff426a88a68855814f/peptable_blat.txt, /home/tana1/workspace/workflow5/work/a6/cefbdb68afbfa3a1d42e82a10ab3d4/parsed_annovar.txt, /home/tana1/workspace/workflow5/work/a8/08cbc8ac3de91507e6e5f62accb5c7/phastcons.txt, /home/tana1/workspace/workflow5/work/73/d5195d4b929919c3ab0cd5799a2d2c/phylocsf.txt, /home/tana1/workspace/workflow5/work/4f/714a7d885220f77c9fa0cf5b4f744f/novpep_perco_quant.txt]
Error executing process > 'mergeSetPeptidetable (1)'
Caused by:
Process mergeSetPeptidetable (1)
terminated with an error exit status (1)
Command executed:
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
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 $varfields| sed 's/ /,/g'
head -n1 peps$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 $'\t' > fixvarpeps cat fixheader fixvarpeps > nov_peptidetable.txt
Command exit status: 1
Command output: (empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Traceback (most recent call last):
File "/home/tana1/workspace/workflow5/bin/group_novpepToLoci.py", line 52, in
Work dir: /home/tana1/workspace/workflow5/work/28/51586263d5a26bb027801bbbb30c41
Tip: when you have fixed the problem you can continue the execution adding the option -resume
to the run command line
Hi,
I am trying to run this pipeline, but i had some errors. I could not find solution. Could anyone help me? I am extremely beginner of this program.
My environment is below; Host PC: Windows10 Pro GuestOS: CentOS8 (virtualbox) Java: JDK11 Nextflow: latest version (today, downloaded) Pipeline: downloaded latest version (5-days-ago updated)
Error log (partially)
Error1 (For this error, i could not find a file that contains this URL) Dec-09 19:38:09.879 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Dec-09 19:38:31.040 [Actor Thread 3] ERROR nextflow.extension.OperatorEx - @unknown java.net.URISyntaxException: Illegal character in scheme name at index 0: %3CindexedmzML%20xmlns=%22http://psi.hupo.org/ms/mzml%22%20xmlns:xsi=%22http://www.w3.org/2001/XMLSchema-instance%22%20xsi:schemaLocation=%22http://psi.hupo.org/ms/mzml%20http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd%22%3E at java.base/java.net.URI$Parser.fail(URI.java:2913) at java.base/java.net.URI$Parser.checkChars(URI.java:3084) at...........
Error2 groovy.lang.MissingMethodException: No signature of method: java.util.ArrayList.replaceFirst() is applicable for argument types: (String, String) values: [.*/(\S+).mzML, $1]
Could anyone please tell me how to solve these errors?