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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