Hi all, Thanks a lot for you advices. Here I post the output for running the peptideProphet at the command line:
C:\Inetpub\wwwroot\ISB\data\probidoutput\ipimouse>xinteract - Ninteract.pep.xml -p0.05 -l7 -OAFm -I2 -I3 -I4 -I5 -I6 -I7 analysis100.xml analysis125.xml analy sis150.xml analysis200.xml analysis25.xml analysis460.xml analysis50.xml analysi s500.xml analysis75.xml analysisunbind.xml xinteract (TPP v4.3 JETSTREAM rev 0, Build 200908071234 (MinGW)) running: "C:/Inetpub/tpp-bin/InteractParser "C:/Inetpub/wwwroot/tmp/ a01564/ISB/d ata/probidoutput/ipimouse/interact.pep.xml" "analysis100.xml" "analysis125.xml" "analysis150.xml" "analysis200.xml" "analysis25.xml" "analysis460.xml" "analysis 50.xml" "analysis500.xml" "analysis75.xml" "analysisunbind.xml" -L"7"" file 1: analysis100.xml file 2: analysis125.xml file 3: analysis150.xml file 4: analysis200.xml file 5: analysis25.xml file 6: analysis460.xml file 7: analysis50.xml file 8: analysis500.xml file 9: analysis75.xml file 10: analysisunbind.xml processed altogether 9099 results results written to file c:/Inetpub/wwwroot/tmp/a01564/ISB/data/ probidoutput/ipi mouse/interact.pep.xml direct your browser to http://localhost/interact.pep.shtml command completed in 8 sec running: "C:/Inetpub/tpp-bin/PeptideProphetParser "C:/Inetpub/wwwroot/ tmp/a01564 /ISB/data/probidoutput/ipimouse/interact.pep.xml" MINPROB=0.05 ACCMASS FORCEDIST R MALDI IGNORECHG=2 IGNORECHG=3 IGNORECHG=4 IGNORECHG=5 IGNORECHG=6 IGNORECHG=7" using Accurate Mass Bins maldi mode Ignoring charge 2+ spectra. Ignoring charge 3+ spectra. Ignoring charge 4+ spectra. Ignoring charge 5+ spectra. Ignoring charge 6+ spectra. Ignoring charge 7+ spectra. Forcing output of mixture model (PROBID) adding Accurate Mass mixture distr init with PROBID Trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN PeptideProphet (TPP v4.3 JETSTREAM rev 0, Build 200908071234 (MinGW)) AKeller@ ISB read in 8815 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Iterations: >>>{{{{ At this point the debug popup box appear}}}}} command "C:/Inetpub/tpp-bin/PeptideProphetParser "C:/Inetpub/wwwroot/ tmp/a01564/ ISB/data/probidoutput/ipimouse/interact.pep.xml" MINPROB=0.05 ACCMASS FORCEDISTR MALDI IGNORECHG=2 IGNORECHG=3 IGNORECHG=4 IGNORECHG=5 IGNORECHG=6 IGNORECHG=7" failed: Unknown error command "C:/Inetpub/tpp-bin/PeptideProphetParser "C:/Inetpub/wwwroot/ tmp/a01564/ ISB/data/probidoutput/ipimouse/interact.pep.xml" MINPROB=0.05 ACCMASS FORCEDISTR MALDI IGNORECHG=2 IGNORECHG=3 IGNORECHG=4 IGNORECHG=5 IGNORECHG=6 IGNORECHG=7" exited with non-zero exit code: -1073741819 QUIT - the job is incomplete To Natalie, At v4.3.0, peptideProphet runs smoothly when NOT using the maldi mode. I have tried to install TPP v4.3.1, but using the latest version I can't run peptideProphet at all, even just using xinteract -Ninteract.pep.xml -p0.05 -l7 -O <list iof xml files> Therefore I change back to 4.3.0 Thanks again~ Regards, Melody On Sep 23, 3:56 am, Natalie Tasman <[email protected]> wrote: > Also, consider upgrading to TPP 4.3.1, which contains several bug fixes. > > -Natalie > > On Sep 22, 2009, at 8:32 AM, Brian Pratt wrote: > > > If it's really the same problem, then it's not a surprise that those > > files don't exist, since the protXML file didn't get created, > > because the pepXML file never went through peptideProphet. But that > > doesn't quite sound like what you're describing - check the log to > > make sure of what's really going on. > > > Brian > > > On Tue, Sep 22, 2009 at 1:02 AM, Melody Lam <[email protected]> > > wrote: > > > Hi all! > > > I have encountered the same problem. I am also using TPP v4.3.0 on > > Windows XP. > > > The output file "interact.prot.shtml" and the stylesheet > > "interact.prot.xsl" files are not found in the directory of the input > > file "interact.pep.xml". > > However, by manually running the following line in the command prompt: > > c:\Inetpub\tpp-bin\protxml2html.pl -file directory/interact.prot.xml > > The output file interact.prot.shtml works as expected. > > > I just wonder why throught the GUI the above command is not executed. > > > Regards, > > Melody > > > On Sep 18, 2:22 am, Brian Pratt <[email protected]> wrote: > > > It appears to have never been run though peptideProphet. > > > > I should add a bit of logic to proteinProphet to catch that and > > issue a more > > > useful error message. > > > > On Thu, Sep 17, 2009 at 10:52 AM, Brian Pratt > > <[email protected]>wrote: > > > > > I'll have a quick look at this. > > > > > Brian > > > > > On Thu, Sep 17, 2009 at 12:13 AM, YAN <[email protected]> > > wrote: > > > > >> Hi everyone! > > > >> Here are some more supplementary information from the output > > screen of > > > >> TPP: > > > > >> Command 1 > > > > >> c:\Inetpub\tpp-bin\ProteinProphet c:/Inetpub/wwwroot/ISB/data/ > > > >> probidoutput/ipimouse/interact.pep.xml c:/Inetpub/wwwroot/ISB/ > > data/ > > > >> probidoutput/ipimouse/interact.prot.xml > > > -------------------------------------------------------------------------------- > > > > >> Command FAILED > > > > >> Command 2 [Thu Sep 17 14:33:13 2009] [ Show / Hide ] > > > > >> c:\Inetpub\tpp-bin\protxml2html.pl -file c:/Inetpub/wwwroot/ > > ISB/data/ > > > >> probidoutput/ipimouse/interact.prot.xml HTML > > > -------------------------------------------------------------------------------- > > > > >> ProteinProphet (C++) by Insilicos LLC and LabKey Software, > > after the > > > >> original Perl by A. Keller (TPP v4.3 JETSTREAM rev 0, Build > > > >> 200908071234 (MinGW)) > > > >> (xml input) (report Protein Length) (using degen pep info) > > > >> . . . reading in c:/Inetpub/wwwroot/ISB/data/probidoutput/ > > ipimouse/ > > > >> interact.pep.xml. . . > > > >> . . . read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra > > with > > > >> min prob 0.05 > > > >> no data - quittingEND OUTPUT > > > >> Writing results to html file: c:/Inetpub/wwwroot/ISB/data/ > > probidoutput/ > > > >> ipimouse/interact.prot.html > > > >> Command FAILED > > > >> ................................................ > > > > >> I am running TPP on Windows XP and I just wonder why the > > program can't > > > >> read the data from the pepxml file. > > > >> I have also uploaded the pepXML file to this group at > > > >>http://groups.google.com/group/spctools-discuss/web/yan.zip > > > > >> Thanks a lot! > > > >> Yan --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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