If you are running the tpp on the commandline you can correct this problem in the omssa output by running the steps of xinteract separately and enabling InteractParser option -P.
On 7/2/09, Jimmy Eng <[email protected]> wrote: > > 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 >> >> > > > > > > -- Sent from my mobile device --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
