Hello, It looks like your search did not produce good results, as evidenced by the "WARNING: Mixture model quality test failed" for all charges. Did you open the tandem results to verify that there were good hits? (i.e. with low expect scores) Another potential issue is that your filename contains a period; for best compatibility with our tools we recommend that you do not use periods for anything else other than the file extension -- so maybe rename the output file to something like "M5-interact.pep.xml". Hope this helps, --Luis
On Sun, Nov 17, 2013 at 8:00 AM, user1 <[email protected]>wrote: > Hello! > > I have a problem with running peptide/protein prophet. Below, you can find an > error message. I havent got this problem previously. I have run so far many > files, but now, there are some which dint want to be processed. The search > with tandem is correct, I havnet got any messaage. Now, the interact.pep.xml > is created, but is empty and interact.prot.xml is not created. Any idea what > can be wrong? > > thanks! > > c:\Inetpub\tpp-bin\xinteract (TPP v4.6 OCCUPY rev 3, Build 201307241109 > (MinGW)) > > running: "C:/Inetpub/tpp-bin/InteractParser "M5.interact.pep.xml" > "M5.tandem.pep.xml" -I -L"6"" > file 1: M5.tandem.pep.xml > SUCCESS: CORRECTED data file c:/Inetpub/wwwroot/ISB/data/Membrane/M5.mzML in > msms_run_summary tag ... > Unknown file type. No file loaded. > processed altogether 53699 results > INFO: Results written to file: > c:/Inetpub/wwwroot/ISB/data/Membrane/M5.interact.pep.xml > command completed in 168 sec > > running: "C:/Inetpub/tpp-bin/DatabaseParser "M5.interact.pep.xml"" > command completed in 0 sec > > running: "C:/Inetpub/tpp-bin/RefreshParser "M5.interact.pep.xml" > "c:/Inetpub/wwwroot/ISB/data/dbase/BCaRun_301013/CONCAT_Uniprot_reviewed_human_301013.fasta"" > - Searching the tree... > - Linking duplicate entries... - Printing results... > > - Building Commentz-Walter keyword tree...command completed in 23 sec > > running: "C:/Inetpub/tpp-bin/PeptideProphetParser "M5.interact.pep.xml" > MINPROB=0.05 ACCMASS DECOY=DECOY_" > using Accurate Mass Bins > 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: UNKNOWN, > Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive detector > > PeptideProphet (TPP v4.6 OCCUPY rev 3, Build 201307241109 (MinGW)) > AKeller@ISB > read in 0 1+, 33305 2+, 17324 3+, 2755 4+, 312 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > Found 26821 Decoys, and 26875 Non-Decoys > Iterations: .........10.........20......... > 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 30 iterations > command completed in 105 sec > > running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i M5.interact.pep.xml -d > "DECOY_"" > Analyzing M5.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/Membrane/M5 (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/Membrane/M5.interact.pep.xml" > > command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > c:/Inetpub/wwwroot/ISB/data/Membrane/M5.interact.pep.xml" failed: Unknown > error > > command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > c:/Inetpub/wwwroot/ISB/data/Membrane/M5.interact.pep.xml" exited with > non-zero exit code: -1073741819 > QUIT - the job is incomplete > > command "c:\Inetpub\tpp-bin\xinteract -NM5.interact.pep.xml -p0.05 -l6 -PREC > -OApu -dDECOY_ M5.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/groups/opt_out. > -- 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/groups/opt_out.
