Thanks for the quick reply! Jimmy's command worked like a charm.
Thanks! On Saturday, April 24, 2021 at 12:43:50 PM UTC-4 Jimmy Eng wrote: > 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/ea686319-cd9e-4b69-befe-9b41d247fe30n%40googlegroups.com.
