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 -
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