Damian, As David noted, in Comet 2020 I unfortunately got rid of a search score that causes the behavior you're seeing. And yes, if I could go back in time, I would not have made that change again because of this noted issue. As a quick intermediate fix until you've updated to the TPP 6 release, run this command on your pep.xml files which should then allow them to be processed through the older TPP versions.
perl -i -pe 's/<search_score name="deltacn"/<search_score name="deltacnstar" value="0.0"\/>\n <search_score name="deltacn"/g;' yourfile.pep.xml On Sat, Apr 24, 2021 at 9:09 AM dfermin <[email protected]> wrote: > 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 > <https://groups.google.com/d/msgid/spctools-discuss/abbd5d1d-8ee8-4231-a488-5c367cbbc705n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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/CAJqD6EMLvskZByN7f8XoSa1M60QhOxfPNo3_OrKYPCFsCMvaqA%40mail.gmail.com.
