Hello Melody, It is possible I forgot to check in one other file that required a change. I will let you know when I get my code merged since it contains other changes I don't want to commit to the repository yet.
On a separate note have you tried using a different search engine (e.g. XTandem) on your data? When I analyzed the data you sent me it appears that mixture models are rather poor and are perhaps reflective of a different problem with the data / search parameters. Can you please double check this? Thanks, -David 2009/9/25 Melody Lam <[email protected]>: > > Hi David, > I've downloaded the code and build the subversion. However, the > problem still exists. > Here are some debug traces attached: > > Key: > At XXXXXX\XXXXX\.h <- It means the file name involved > > My thoughts at indicated at the comment /* ?????? */ > > Thanks again! > > Regards, > Melody > > > At .\trans_proteomic_pipeline\src\common\array.h > > inline int length() const { // synonym for size() (it's evil to have > synonyms! but changing code is bad too) > return iUsed_; /* Error here */ > } > > ============================================= > > At .\trans_proteomic_pipeline\src\validation\mixturedistribution > \decaycontinuousmultimixturedistr.cxx > > double DecayContinuousMultimixtureDistr::getMixtureProb(int index, > double val = -999.0) { > > if(index >= vals_->length()) /* Trace back to this step, vals is > NOT initialized */ > return getProb(val); > return getMixtureProbWithNTT(ntt_->getNTTValue(index), index); > } > > ============================================= > > At .\trans_proteomic_pipeline\src\validation\discriminatefunction > \discrimvalmixturedistr.cxx > > if(qtof_ || (maldi_ && charge_ == 0)) { > //cerr << "pos prob: " << ((DecayContinuousMultimixtureDistr*) > (posdistr_))->getMixtureProb(index, (*doublevals_)[index]) << endl; / > * Seems to be problems with posdistr_ */ > //if(((DecayContinuousMultimixtureDistr*)(posdistr_))->oneProb > ((*doublevals_)[index])) { > // return 1.0; > //} > > return ((DecayContinuousMultimixtureDistr*)(posdistr_))- >>getMixtureProb(index, (*doublevals_)[index]); > > > //cerr << "MALDI" << endl; > //cerr << "number of distrs in DISCRIMVAL: " << > ((DecayContinuousMultimixtureDistr*)(posdistr_))->getNumDistributions > () << endl; > } > > > ======================================== > > On 9月24日, 下午11時43分, 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- 隱藏被引用文字 - >> >> - 顯示被引用文字 - > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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