This error can be safely ignored. It comes up because there is not decoy tag specified when ProtProphModel.pl runs. You are correct that this is no way to fail, this will be corrected in the future. Luis already pointed to the problem so this would be a quick fix.
-David 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. 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 -~----------~----~----~----~------~----~------~--~---
