Hi Andreas,Try to re-run only ProteinProphet directly (not via xinteract) on the existing PeptideProphet results, and see if they match the ones you already have, or if you get any errors. Cheers, --Luis
On Tue, Sep 22, 2009 at 10:27 AM, Andreas Quandt <[email protected]>wrote: > hey luis, > > i am not really sure if the results are okay or not (as there are far too > many proteins in these results ;-) ) > the file is successfully rendered by petunia but if the file has been fully > created, i cannot judge :-( . > > > cheers, > andreas > > > > On Tue, Sep 22, 2009 at 7:14 PM, Luis Mendoza <[email protected] > > wrote: > >> The error seems to be coming from ProtProphModels.pl: >> >> Illegal division by zero at /usr/local/apps/tpp/bin/ProtProphModels.pl line >> 231. >> >> >> But it seems that ProteinProphet finished; do those results look ok? >> --Luis >> >> >> >> On Tue, Sep 22, 2009 at 9:57 AM, Andreas Quandt <[email protected] >> > wrote: >> >>> dear list, >>> >>> >>> i tried to process several files with spectrast but get this error code >>> which unfortunately tells me nothing :-( >>> >>> >>> hopefully one of you can help me out here ... >>> >>> >>> cheers, >>> andreas >>> >>> p.s. the output of the xinteract run looked as follow: >>> >>> >>> /usr/local/apps/tpp/bin/xinteract (TPP v4.3 JETSTREAM rev 1, Build >>> 200909181208 (linux)) >>> >>> running: "/usr/local/apps/tpp/bin/InteractParser >>> '/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10100_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10105_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10114_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10107_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10093_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10094_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10102_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10096_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10104_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10095_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10111_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10098_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10116_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10099_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10103_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10106_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10112_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10097_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10109_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10108_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10113_c.pep.xml' >>> '/IMSB/results/workflow/158/init/O08-10115_c.pep.xml' -L'7'" >>> >>> >>> >>> file 1: /IMSB/results/workflow/158/init/O08-10100_c.pep.xml >>> file 2: /IMSB/results/workflow/158/init/O08-10105_c.pep.xml >>> file 3: /IMSB/results/workflow/158/init/O08-10114_c.pep.xml >>> file 4: /IMSB/results/workflow/158/init/O08-10107_c.pep.xml >>> >>> >>> >>> file 5: /IMSB/results/workflow/158/init/O08-10093_c.pep.xml >>> file 6: /IMSB/results/workflow/158/init/O08-10094_c.pep.xml >>> file 7: /IMSB/results/workflow/158/init/O08-10102_c.pep.xml >>> file 8: /IMSB/results/workflow/158/init/O08-10096_c.pep.xml >>> >>> >>> >>> file 9: /IMSB/results/workflow/158/init/O08-10104_c.pep.xml >>> file 10: /IMSB/results/workflow/158/init/O08-10095_c.pep.xml >>> file 11: /IMSB/results/workflow/158/init/O08-10111_c.pep.xml >>> file 12: /IMSB/results/workflow/158/init/O08-10098_c.pep.xml >>> >>> >>> >>> file 13: /IMSB/results/workflow/158/init/O08-10116_c.pep.xml >>> file 14: /IMSB/results/workflow/158/init/O08-10099_c.pep.xml >>> file 15: /IMSB/results/workflow/158/init/O08-10103_c.pep.xml >>> file 16: /IMSB/results/workflow/158/init/O08-10106_c.pep.xml >>> >>> >>> >>> file 17: /IMSB/results/workflow/158/init/O08-10112_c.pep.xml >>> file 18: /IMSB/results/workflow/158/init/O08-10097_c.pep.xml >>> file 19: /IMSB/results/workflow/158/init/O08-10109_c.pep.xml >>> file 20: /IMSB/results/workflow/158/init/O08-10108_c.pep.xml >>> >>> >>> >>> file 21: /IMSB/results/workflow/158/init/O08-10113_c.pep.xml >>> file 22: /IMSB/results/workflow/158/init/O08-10115_c.pep.xml >>> processed altogether 99822 results >>> >>> >>> results written to file >>> /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.shtml >>> >>> >>> >>> >>> >>> command completed in 23 sec >>> >>> running: "/usr/local/apps/tpp/bin/PeptideProphetParser >>> '/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml' >>> DECOY=DECOY_ ACCMASS LEAVE PI INSTRWARN" >>> >>> >>> >>> using Accurate Mass Bins >>> using pI >>> Using no error on different instrument types. >>> Using Decoy Label "DECOY_". >>> (SpectraST) >>> adding Accurate Mass mixture distr >>> adding pI mixture distr >>> init with SpectraST trypsin >>> >>> >>> >>> MS Instrument info: Manufacturer: ThermoFinnigan, Model: LTQ Orbitrap XL, >>> Ionization: ESI, Analyzer: ITMS, Detector: EMT >>> >>> PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909181208 (linux)) >>> akel...@isb >>> read in 0 1+, 75687 2+, 21029 3+, 2960 4+, 146 5+, 0 6+, and 0 7+ spectra. >>> >>> >>> >>> Initialising statistical models ... >>> Iterations: .........10.........20......... >>> model complete after 30 iterations >>> command completed in 79 sec >>> >>> running: "/usr/local/apps/tpp/bin/ProphetModels.pl -i >>> /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml" >>> >>> >>> >>> Analyzing /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml >>> ... >>> Reading Accurate Mass Model model +1 ... >>> Reading kernel density calc pI [pI] model +1 ... >>> Reading Accurate Mass Model model +2 ... >>> >>> >>> >>> Reading kernel density calc pI [pI] model +2 ... >>> Reading Accurate Mass Model model +3 ... >>> Reading kernel density calc pI [pI] model +3 ... >>> Reading Accurate Mass Model model +4 ... >>> Reading kernel density calc pI [pI] model +4 ... >>> >>> >>> >>> Reading Accurate Mass Model model +5 ... >>> Reading kernel density calc pI [pI] model +5 ... >>> Reading Accurate Mass Model model +6 ... >>> Reading kernel density calc pI [pI] model +6 ... >>> Reading Accurate Mass Model model +7 ... >>> >>> >>> >>> Reading kernel density calc pI [pI] model +7 ... >>> Parsing search results "/home/andqua/O08-10100_c (SpectraST)"... >>> => Total of 2389 hits. >>> Parsing search results "/home/andqua/O08-10105_c (SpectraST)"... >>> >>> >>> >>> => Total of 2321 hits. >>> Parsing search results "/home/andqua/O08-10114_c (SpectraST)"... >>> => Total of 1933 hits. >>> Parsing search results "/home/andqua/O08-10107_c (SpectraST)"... >>> => Total of 1949 hits. >>> >>> >>> >>> Parsing search results "/home/andqua/O08-10093_c (SpectraST)"... >>> => Total of 2660 hits. >>> Parsing search results "/home/andqua/O08-10094_c (SpectraST)"... >>> => Total of 2756 hits. >>> Parsing search results "/home/andqua/O08-10102_c (SpectraST)"... >>> >>> >>> >>> => Total of 2743 hits. >>> Parsing search results "/home/andqua/O08-10096_c (SpectraST)"... >>> => Total of 2813 hits. >>> Parsing search results "/home/andqua/O08-10104_c (SpectraST)"... >>> => Total of 2457 hits. >>> >>> >>> >>> Parsing search results "/home/andqua/O08-10095_c (SpectraST)"... >>> => Total of 2889 hits. >>> Parsing search results "/home/andqua/O08-10111_c (SpectraST)"... >>> => Total of 298 hits. >>> Parsing search results "/home/andqua/O08-10098_c (SpectraST)"... >>> >>> >>> >>> => Total of 454 hits. >>> Parsing search results "/home/andqua/O08-10116_c (SpectraST)"... >>> => Total of 2116 hits. >>> Parsing search results "/home/andqua/O08-10099_c (SpectraST)"... >>> => Total of 1861 hits. >>> >>> >>> >>> Parsing search results "/home/andqua/O08-10103_c (SpectraST)"... >>> => Total of 2690 hits. >>> Parsing search results "/home/andqua/O08-10106_c (SpectraST)"... >>> => Total of 1997 hits. >>> Parsing search results "/home/andqua/O08-10112_c (SpectraST)"... >>> >>> >>> >>> => Total of 492 hits. >>> Parsing search results "/home/andqua/O08-10097_c (SpectraST)"... >>> => Total of 2191 hits. >>> Parsing search results "/home/andqua/O08-10109_c (SpectraST)"... >>> => Total of 743 hits. >>> >>> >>> >>> Parsing search results "/home/andqua/O08-10108_c (SpectraST)"... >>> => Total of 1959 hits. >>> Parsing search results "/home/andqua/O08-10113_c (SpectraST)"... >>> => Total of 921 hits. >>> Parsing search results "/home/andqua/O08-10115_c (SpectraST)"... >>> >>> >>> >>> => Total of 2376 hits. >>> Warning: empty y range [0:0], adjusting to [0:1] >>> >>> plot >>> "/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep_IPPROB.tsv" >>> using 2:1 title "iProphet" with line lc 2 , x notitle with line lt 0 lc -1 >>> >>> >>> >>> >>> ^ >>> "/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep_IPPROB.gp", >>> line 16: warning: Skipping data file with no valid points >>> >>> >>> >>> command completed in 6 sec >>> >>> running: "/usr/local/apps/tpp/bin/DatabaseParser >>> '/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml'" >>> command completed in 1 sec >>> >>> running: "/usr/local/apps/tpp/bin/RefreshParser >>> '/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml' >>> '/IMSB/data/databases/swissprot_57.7/sp_9606.fasta'" >>> >>> >>> >>> - Building Commentz-Walter keyword tree... - Searching the tree... >>> - Linking duplicate entries... - Printing results... >>> >>> command completed in 14 sec >>> >>> running: "/usr/local/apps/tpp/cgi-bin/PepXMLViewer.cgi -I >>> /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml" >>> >>> >>> >>> command completed in 6 sec >>> >>> running: "/usr/local/apps/tpp/bin/ProteinProphet >>> '/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml' >>> '/IMSB/results/workflow/158/spectrast_xinteract/Xinteract.prot.xml' XML" >>> >>> >>> >>> ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the >>> original Perl by A. Keller (TPP v4.3 JETSTREAM rev 1, Build 200909181208 >>> (linux)) >>> (xml input) (report Protein Length) (using degen pep info) >>> . . . reading in >>> /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.pep.xml. . . >>> >>> >>> >>> . . . read in 0 1+, 33817 2+, 8212 3+, 926 4+, 53 5+, 0 6+, 0 7+ spectra >>> with min prob 0.05 >>> INFO: mu=4.69978e-06, db_size=90930969 >>> >>> protein probabilities written to file >>> /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.prot.xml >>> >>> >>> >>> direct your browser to >>> http://cal//IMSB/results/workflow/158/spectrast_xinteract/Xinteract.prot.shtml >>> >>> command completed in 71 sec >>> >>> >>> >>> running: "/usr/local/apps/tpp/bin/ProtProphModels.pl -i >>> /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.prot.xml" >>> Illegal division by zero at /usr/local/apps/tpp/bin/ProtProphModels.pl line >>> 231. >>> >>> >>> >>> Analyzing /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.prot.xml >>> ... >>> >>> command "/usr/local/apps/tpp/bin/ProtProphModels.pl -i >>> /IMSB/results/workflow/158/spectrast_xinteract/Xinteract.prot.xml" exited >>> with non-zero exit code: 6400 >>> >>> >>> >>> QUIT - the job is incomplete >>> >>> >>> >>> >> >> >> > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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