Hello I performed a search on 4 mzML files against a human proteome file with decoys appended. The decoy prefix I'm using is 'rev_'
I ran comet version 2020.01 rev 3 on the mzML file and got out the comet-generated pep.xml files. When I run xinteract on these files PeptideProphet seems unable to find any spectra. I've looked at the pep.xml files comet generated and it has all the usual features. The files contain the top 5 hits for each spectra. Any suggestions what might be wrong? Thanks in advance for any and all help. I'm running TPP v5.2.0 on a Centos 7 box in case it helps Here is the stdout on the terminal: #================================================================== [dfermin tmp]$ xinteract -Opwd -drev *.pep.xml xinteract (TPP v5.2.0 Flammagenitus, Build 201904020842-exported (Linux-x86_64)) running: "/usr/local/apps/tpp/bin/InteractParser 'interact.pep.xml' '01347_H01_P013678_S00_N08_R2.pep.xml' '01347_H02_P013678_S00_N16_R2.pep.xml' '01347_H03_P013678_S00_N24_R2.pep.xml' '01347_H04_P013678_S00_N32_R2.pep.xml' -L'7'" file 1: 01347_H01_P013678_S00_N08_R2.pep.xml file 2: 01347_H02_P013678_S00_N16_R2.pep.xml file 3: 01347_H03_P013678_S00_N24_R2.pep.xml file 4: 01347_H04_P013678_S00_N32_R2.pep.xml processed altogether 203112 results INFO: Results written to file: /nfs/md0/testRun2021/interact.pep.xml command completed in 104 sec running: "/usr/local/apps/tpp/bin/DatabaseParser 'interact.pep.xml'" command completed in 1 sec running: "/usr/local/apps/tpp/bin/RefreshParser 'interact.pep.xml' '/nfs/md0/tpp.data/human_uniprot_withIsoforms.2021-04-14.plusREV.fa'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 62 sec running: "/usr/local/apps/tpp/bin/PeptideProphetParser 'interact.pep.xml' INSTRWARN DECOYPROBS DECOY=rev" Using no error on different instrument types. Using Decoy Label "rev". Decoy Probabilities will be reported. (Comet) init with Comet trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.2.0 Flammagenitus, Build 201904020842-exported (Linux-x86_64)) AKeller@ISB read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. read in no data command "/usr/local/apps/tpp/bin/PeptideProphetParser 'interact.pep.xml' INSTRWARN DECOYPROBS DECOY=rev" exited with non-zero exit code: 256 QUIT - the job is incomplete -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/abbd5d1d-8ee8-4231-a488-5c367cbbc705n%40googlegroups.com.
