Hey David Many thanks for the explanation :-)
Cheers Andreas On Sep 22, 2009, at 7:44 PM, David Shteynberg <[email protected] > wrote: > > 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. 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