Dear David, I have updated the search parameter in ProbID and I have uploaded the output files to ftp://ftp.systemsbiology.net/incoming/melody_lam.rar
I have tried to use XTandem on this dataset and I can find about 300 proteins. Thanks a lot for your help! Regards, Melody On Oct 6, 1:10 am, David Shteynberg <[email protected]> wrote: > 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 > > ... > > read more >> --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
