Hi Mike, With Kojak data the peptide length is meaningless and recorded as zero in the pepXML. The default parameters of xinteract use min peptide length of 7 which invalidates all results in this file. You have to run with min peptide length of zero when processing Kojak data: xinteract -l0
Cheers! -David On Mon, Nov 14, 2022 at 5:06 PM Michael Riffle <[email protected]> wrote: > Greetings TPP folks, > > I just pulled the latest Docker image and am trying to run the Kojak then > PeptideProphet. Kojak runs fine, PeptideProphet produces an error. Here is > my output: > > ``` > sudo docker run -v `pwd`:/data spctools/tpp xinteract > QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml > > xinteract (TPP v6.1.0 Parhelion, Build 202206071715-8676 (Linux-x86_64)) > > running: "/usr/local/tpp/bin/InteractParser 'interact.pep.xml' > 'QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml' -L'7'" > file 1: QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml > processed altogether 77134 results > INFO: Results written to file: /data/interact.pep.xml > command completed in 5 sec > > running: "/usr/local/tpp/bin/DatabaseParser 'interact.pep.xml'" > command completed in 1 sec > > running: "/usr/local/tpp/bin/RefreshParser 'interact.pep.xml' > '/data/EH217_3pepCnt_plusRev.fasta'" > enzyme name is:trypsin > - Building Commentz-Walter keyword tree... > - Searching the tree... > - Linking duplicate entries... > - Printing results... > - Mapped 42490 entries > > command completed in 3 sec > using MAXEHFX_2019_0510_AZ_034_eh220_comet.pep.xml for PeptideProphet... > > running: "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'" > (Kojak) > init with Kojak trypsin > init Loop model with Kojak trypsin > adding XLSecondScoreFraction mixture distribution > adding XLTopExpectScore mixture distribution > init XL model with Kojak trypsin > PeptideProphet (TPP v6.1.0 Parhelion, Build 202206071715-8676 > (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 > MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: > UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN > > INFO: Processing xl MixtureModel ... > > command "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'" > exited with non-zero exit code: 256 > QUIT - the job is incomplete > ``` > > I suspect the "read no data" line above, towards the end, is the culprit, > but I can't guess what might be causing that. Do you have any ideas? > > Thanks, > Mike Riffle > > > -- > 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/ee50b09f-4a8a-42f8-9eb3-1705200196a4n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/ee50b09f-4a8a-42f8-9eb3-1705200196a4n%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/CAGJJY%3D_3ekAJcxxh7-gokixvLc2yZ0H8uZ-35880QcdVYqOuug%40mail.gmail.com.
