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lehtiolab / proteogenomics-analysis-workflow

IPAW: a Nextflow workflow for proteogenomics
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Error: java.net.URISyntaxException #9

Closed TnakaNY closed 4 years ago

TnakaNY commented 4 years ago

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?

TnakaNY commented 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

glormph commented 4 years ago

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) ).

TnakaNY commented 4 years ago

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

TnakaNY commented 4 years ago

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

TnakaNY commented 4 years ago

Even though i started the container, i received same errors (above).

glormph commented 4 years ago

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.

TnakaNY commented 4 years ago

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

glormph commented 4 years ago

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 :)

TnakaNY commented 4 years ago

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 -

glormph commented 4 years ago

Exactly, those are run in other circumstances, when you prefractionate using isoelectric focusing.

TnakaNY commented 4 years ago

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:

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 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:

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: 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 peplist.sort(key=lambda x:list(map(int,(x.chr,x.start)))) File "/home/tana1/workspace/workflow5/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/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