Hi, I'm using TPP v4.2 JETSTREAM rev 1 built on Fedora Core 8 and am having a problem with ProteinProphet never finishing when run on data from 2 particular input files combined.
Xinteract is run on 2 .pep.xml files previously converted from Mascot search results: xinteract -Ninteract.pep.xml -E656 -p0 -dDECOY -O-d-pA *.pep.xml Everything is fine up until ProteinProphet, which sits there using 100% cpu and never completes. Output of ProteinProphet is just: ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.2 JETSTREAM rev 1, Build 200904281542 (linux)) (xml input) (report Protein Length) (using degen pep info) . . . reading in /diskb/cpfp_data/live/search_results/2700/2737/ interact.pep.xml. . . . . . read in 0 1+, 1561 2+, 1855 3+, 734 4+, 147 5+, 6 6+, 0 7+ spectra with min prob 0.05 If I run ProteinProphet stand-alone on interact.pep.xml I have the same problem. The input files don't seem to be anything special... they represent Mascot searches of two Orbitrap runs on a given complex fraction. Inidividually they will run through xinteract / proteinprophet without problems. The .pep.xml file for the combined xinteract looks fine. It's just ProteinProphet that appears to have a problem. There are no such problems with any of the other 10 fractions, which each have 2 runs/searches that combine without problem, producing ProteinProphet results as expected. Any hints about what to look at to try and solve this would be much appreciated. Dave Trudgian --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
