One of my data failed and the return code 65280. The details are copied below.
I noticed that I have more decoys than non-decoys. However, I found many good MS2 spectra when I manually check my raw data. What settings should I use to get the real good peptides validated through TPP (I used semi- when I did the database search using X!Tandem)? Thanks. Xianyin. ------------------------------------------------------------------------------------------------------------------------------------------------------- c:\Inetpub\tpp-bin\xinteract (TPP v4.6 OCCUPY rev 3, Build 201307241109 (MinGW)) PPM mode in Accurate Mass Model ... running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "20140307_12A.tandem.pep.xml" -L"7"" file 1: 20140307_12A.tandem.pep.xml SUCCESS: CORRECTED data file c:/Inetpub/wwwroot/ISB/data/20140307_12A.mzXML in msms_run_summary tag ... processed altogether 22005 results INFO: Results written to file: c:/Inetpub/wwwroot/ISB/data/interact.pep.xml command completed in 6 sec running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" command completed in 1 sec running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" "c:/Inetpub/wwwroot/ISB/data/RAT20140219T_DECOY.fasta"" - Searching the tree... - Linking duplicate entries... - Printing results... - Building Commentz-Walter keyword tree...command completed in 9 sec running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" MINPROB=0.05 PPM ACCMASS DECOY=DECOY" using Accurate Mass Bins using PPM mass difference Using Decoy Label "DECOY". (X! Tandem (k-score)) adding Accurate Mass mixture distr init with X! Tandem (k-score) trypsin MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ Orbitrap Velos, Ionization: electrospray ionization, Analyzer: radial ejection linear ion trap, Detector: electron multiplier PeptideProphet (TPP v4.6 OCCUPY rev 3, Build 201307241109 (MinGW)) AKeller@ISB read in 0 1+, 6945 2+, 6638 3+, 4461 4+, 3930 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Found 11360 Decoys, and 10614 Non-Decoys Iterations: .........10.........20.........30.. WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). model complete after 33 iterations command completed in 34 sec running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml -d "DECOY"" Analyzing interact.pep.xml ... Reading Accurate Mass Model model +1 ... Reading Accurate Mass Model model +2 ... Reading Accurate Mass Model model +3 ... Reading Accurate Mass Model model +4 ... Reading Accurate Mass Model model +5 ... Reading Accurate Mass Model model +6 ... Reading Accurate Mass Model model +7 ... Parsing search results "c:/Inetpub/wwwroot/ISB/data/20140307_12A (X! Tandem (k-score))"... => Found 0 hits. (0 decoys, 0 excluded) => Total so far: 0 hits. (0 decoys, 0 excluded) The system cannot find the path specified. command completed in 1 sec running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/interact.pep.xml" command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/interact.pep.xml" failed: Unknown error command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/Inetpub/wwwroot/ISB/data/interact.pep.xml" exited with non-zero exit code: 255 QUIT - the job is incomplete command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -PPM -OAp -dDECOY 20140307_12A.tandem.pep.xml" failed: Unknown error -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
