Hi, I have seen something similar in some cases but when using X! tandem branch and selecting the option of "Use Gamma distribution to model the negatives" since this option is unique to X!tandem I don't know if and how this is related to what you obsevered but the outcome and the extact stage are identical. I hope that might help. Oded
On Mar 13, 8:34 pm, "Dave @ UPENN" <[email protected]> wrote: > Hey, > I've never encountered this before but when i try to run xinteract, > peptideprophet hangs during the initializing stats step. i tried > fooling around with the settings with no avail. i tried omitting the - > Od, adding -l1, and -p0. Any ideas what could be happening here? > > Thanks! > > here's the output: > > $ /opt/tpp/`uname -p`/bin/xinteract -Ninteract.xml -Old -dREV *.xml > > /opt/tpp/x86_64/bin/xinteract (TPP v4.1 JETSTREAM rev 1, Build > 200812051718 (linux)) > > running: "/opt/tpp/x86_64/bin/InteractParser 'interact.xml' > 'CGB-001-289U.pep.xml' 'CGB-001-289V.pep.xml' 'CGB-001-289W.pep.xml' > 'CGB-001-289Y.pep.xml' 'CGB-001-289Z.pep.xml' 'CGB-001-299A.pep.xml' > 'CGB-001-299B.pep.xml' 'CGB-001-299C.pep.xml' 'CGB-001-299D.pep.xml' > 'CGB-001-299E.pep.xml' 'CGB-001-299F.pep.xml' 'CGB-001-299U.pep.xml' > 'CGB-001-299V.pep.xml' 'CGB-001-299W.pep.xml' 'CGB-001-299X.pep.xml' > 'CGB-001-299Y.pep.xml' 'CGB-001-299Z.pep.xml' 'CGB-001-300A.pep.xml' > 'CGB-001-300B.pep.xml' 'CGB-001-300C.pep.xml' 'CGB-001-300D.pep.xml' > 'CGB-001-300E.pep.xml' 'CGB-001-300F.pep.xml' 'CGB-001-300U.pep.xml' > 'CGB-001-300V.pep.xml' 'CGB-001-300W.pep.xml' 'CGB-001-300X.pep.xml' > 'CGB-001-300Y.pep.xml' 'CGB-001-301A.pep.xml' 'CGB-001-301B.pep.xml' > 'CGB-001-301C.pep.xml' 'CGB-001-301D.pep.xml' 'CGB-001-301E.pep.xml' > 'CGB-001-301F.pep.xml' 'CGB-001-301U.pep.xml' 'CGB-001-301V.pep.xml' > 'CGB-001-301W.pep.xml' 'CGB-001-301X.pep.xml' 'CGB-001-301Y.pep.xml' > 'CGB-001-301Z.pep.xml' 'CGB-002-297A.pep.xml' 'CGB-002-297B.pep.xml' > 'CGB-002-297C.pep.xml' 'CGB-002-297D.pep.xml' 'CGB-002-297E.pep.xml' > 'CGB-002-297F.pep.xml' 'CGB-002-297U.pep.xml' 'CGB-002-297V.pep.xml' > 'CGB-002-297W.pep.xml' 'CGB-002-297X.pep.xml' 'CGB-002-297Y.pep.xml' > 'CGB-002-297Z.pep.xml' 'CGB-002-298A.pep.xml' 'CGB-002-298B.pep.xml' > 'CGB-002-298C.pep.xml' 'CGB-002-298D.pep.xml' > 'CGB-002-298E_080307154954.pep.xml' 'CGB-002-298E.pep.xml' > 'CGB-002-298F_080307173448.pep.xml' 'CGB-002-298F.pep.xml' > 'interact.xml' -L'7'" > Skipping file interact.xml, which has the same name as the output > file ... > file 1: CGB-001-289U.pep.xml > file 2: CGB-001-289V.pep.xml > file 3: CGB-001-289W.pep.xml > file 4: CGB-001-289Y.pep.xml > file 5: CGB-001-289Z.pep.xml > file 6: CGB-001-299A.pep.xml > file 7: CGB-001-299B.pep.xml > file 8: CGB-001-299C.pep.xml > file 9: CGB-001-299D.pep.xml > file 10: CGB-001-299E.pep.xml > file 11: CGB-001-299F.pep.xml > file 12: CGB-001-299U.pep.xml > file 13: CGB-001-299V.pep.xml > file 14: CGB-001-299W.pep.xml > file 15: CGB-001-299X.pep.xml > file 16: CGB-001-299Y.pep.xml > file 17: CGB-001-299Z.pep.xml > file 18: CGB-001-300A.pep.xml > file 19: CGB-001-300B.pep.xml > file 20: CGB-001-300C.pep.xml > file 21: CGB-001-300D.pep.xml > file 22: CGB-001-300E.pep.xml > file 23: CGB-001-300F.pep.xml > file 24: CGB-001-300U.pep.xml > file 25: CGB-001-300V.pep.xml > file 26: CGB-001-300W.pep.xml > file 27: CGB-001-300X.pep.xml > file 28: CGB-001-300Y.pep.xml > file 29: CGB-001-301A.pep.xml > file 30: CGB-001-301B.pep.xml > file 31: CGB-001-301C.pep.xml > file 32: CGB-001-301D.pep.xml > file 33: CGB-001-301E.pep.xml > file 34: CGB-001-301F.pep.xml > file 35: CGB-001-301U.pep.xml > file 36: CGB-001-301V.pep.xml > file 37: CGB-001-301W.pep.xml > file 38: CGB-001-301X.pep.xml > file 39: CGB-001-301Y.pep.xml > file 40: CGB-001-301Z.pep.xml > file 41: CGB-002-297A.pep.xml > file 42: CGB-002-297B.pep.xml > file 43: CGB-002-297C.pep.xml > file 44: CGB-002-297D.pep.xml > file 45: CGB-002-297E.pep.xml > file 46: CGB-002-297F.pep.xml > file 47: CGB-002-297U.pep.xml > file 48: CGB-002-297V.pep.xml > file 49: CGB-002-297W.pep.xml > file 50: CGB-002-297X.pep.xml > file 51: CGB-002-297Y.pep.xml > file 52: CGB-002-297Z.pep.xml > file 53: CGB-002-298A.pep.xml > file 54: CGB-002-298B.pep.xml > file 55: CGB-002-298C.pep.xml > file 56: CGB-002-298D.pep.xml > file 57: CGB-002-298E_080307154954.pep.xml > file 58: CGB-002-298E.pep.xml > file 59: CGB-002-298F_080307173448.pep.xml > file 60: CGB-002-298F.pep.xml > processed altogether 114484 results > > results written to file /data/www/htdocs/qInteract/data2/ > tilo_20081214124503/tilo_3527/interact.shtml > > command completed in 23 sec > > running: "/opt/tpp/x86_64/bin/PeptideProphetParser 'interact.xml' > LEAVE DECOYPROBS DECOY=REV" > Using Decoy Label "REV". > Decoy Probabilities will be reported. > (SEQUEST) (leaving deltacn* entries) > init with SEQUEST trypsin > MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ FT, > Ionization: ESI, Analyzer: FTMS, Detector: unknown > > PeptideProphet (TPP v4.1 JETSTREAM rev 1, Build 200812051718 > (linux)) akel...@isb > read in 28141 1+, 33067 2+, 7493 3+, 314 4+, and 13 5+ spectra > Initialising statistical models ... --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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