David, Thanks a lot for your response. I generated the decoy database and rerun the OMSSA earlier.
I run the command line manually. And as you suggested, I used option - p for InteractParser, but when I run PeptideProphetParse, got this error: ERROR: NAN probability density detected. Please alert the developer !!! I will try Jimmy's suggestion and see how it goes. Thanks again! Ping On Jul 2, 7:15 pm, David Shteynberg <[email protected]> wrote: > If you are running the tpp on the commandline you can correct this > problem in theomssaoutput by running the steps of xinteract > separately and enabling InteractParser option -P. > > On 7/2/09, Jimmy Eng <[email protected]> wrote: > > > > > > > Ping, > > > I just downloadedOMSSA2.1.4 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,OMSSAseems 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 theomssapep.xml output files. my > >>omssa'sversion 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 forOMSSAis 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 withOMSSATrypsin > >> 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 -~----------~----~----~----~------~----~------~--~---
