Hi David! Sorry for the multiple message sent. I've removed those repeating messages. Thanks David for fixing the problem. I'll try to build the files. Thanks again. Regards, Melody
On Sep 24, 11:43 pm, dshteynberg <[email protected]> wrote: > Hi Melody, > > I've tracked down and fixed the bug using the files you sent. My new > code is in the sashimi subversion code repository. Maybe someone can > build the PeptideProphetParser executable on windows and share that > with you until a new release is made available that includes this fix. > > Thanks, > > -David > > On Thu, Sep 24, 2009 at 1:15 AM, Melody Lam <[email protected]> wrote: > > > 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 tohttp://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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