Ping, I just downloaded OMSSA 2.1.4 and tried the direct pep.xml export myself. I do see a problem with the resulting pep.xml file that the "-op" option generates that's causing the problem you're seeing.
The key error message in your output is this: WARNING: No decoys with label DECOY were found in this dataset. Looking at the generated pep.xml files, OMSSA seems to be placing some number in the protein="" attribute of each search_hit element. Whereas PeptideProphet expects this protein attribute to contain some protein identifier that includes the DECOY string for those decoy matches. In the converters we use, the value of the protein attribute is the first word of the protein definition line. As for a fix, we need someone at NCBI to address this and hopefully someone here will contact them about this. For you in the short term, you're going to need a developer to modify you pep.xml files to replace the value in the "protein" attribute with the first word from the "protein_descr" attribute of each search_hit entry. - Jimmy Ping wrote: > Hi, > > I am trying to run the xinteract on the omssa pep.xml output files. my > omssa's version is 2.1.4, my TPP version is 4.2.1. But I couldn't get > it through. I search the old post, there is a similar post, but the > problem was solved by specifying enzyme to xinteract. > > I tried it, but is still not working. InteractParse went through, but > PeptideProphetParser got stuck by a segmentation fault. > > Any help would be greatly appreciated! > > Many Thanks, > > Ping > > ***** output for interactParser and PeptideProphetParser > > InteractParser 'interact.pep.xml' 'omssa.pep.xml' -L'7' -E'trypsin' -C > -P > file 1: ParoSaliv_SHAM_03.pep.xml > processed altogether 2623 results > > PeptideProphetParser 'interact.pep.xml' DECOY=DECOY MINPROB=0 > NONPARAM > Using Decoy Label "DECOY". > Using non-parametric distributions > (OMSSA) (minprob 0) > WARNING!! The discriminant function for OMSSA is not yet complete. It > is presented here to help facilitate trial and discussion. Reliance > on this code for publishable scientific results is not recommended. > init with OMSSA Trypsin > MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: > UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN > > PeptideProphet (TPP v4.2 JETSTREAM rev 1, Build 200905131510 > (linux)) akel...@isb > read in 75 1+, 1790 2+, 749 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > WARNING: No decoys with label DECOY were found in this dataset. > reverting to fully unsupervised method. > Iterations: .........10.........20 > Segmentation fault > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
