Hi Jagan, Thanks for the thorough bug report. Have you tried the latest version? The RT or PI models had bug that have been fixed since July. Also if you want to upload these search results I can try tracing the latest code on it.
Cheers, -David On Sun, Feb 6, 2011 at 4:53 PM, Jagan Kommineni <[email protected]>wrote: > Dear All, > > Here are first few lines of the the Mascot Search ... > ========================================================================== > Mascot Search Results > > *User : Nathan Edwards* > *Email : [email protected]* > *Search title : Conversion of > C:\Users\Nathan\Downloads\sergei_digest_A_full_01.mzXML to mascot generic* > *MS data file : sergei_digest_A_full_01.mgf* > *Database : decoy_SwissProt uniprot_sprot_generic (1038696 > sequences; 366546324 residues)* > *Timestamp : 3 Feb 2011 at 01:44:00 GMT* > *Enzyme : semiTrypsin* > *Fixed modifications : Carbamidomethyl (C)* > *Variable modifications : Gln->pyro-Glu (N-term Q),Glu->pyro-Glu (N-term > E),Oxidation (M),Pyro-carbamidomethyl (N-term C)* > *Mass values : Monoisotopic* > *Protein Mass : Unrestricted* > *Peptide Mass Tolerance : ± 2 Da* > *Fragment Mass Tolerance: ± 0.6 Da* > *Max Missed Cleavages : 1* > *Instrument type : ESI-TRAP* > *Number of queries : 2165* > *Protein hits :** P02666 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit1>* > sp|P02666|CASB_BOVIN Beta-casein OS=Bos taurus GN=CSN2 PE=1 SV=2 * P02755 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit2>* > sp|P02755|LACB_BUBBU Beta-lactoglobulin OS=Bubalus bubalis GN=LGB PE=1 SV=2 > * P02754 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit3>* > sp|P02754|LACB_BOVIN Beta-lactoglobulin OS=Bos taurus GN=LGB PE=1 SV=3 * > P00921 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit4>* > sp|P00921|CAH2_BOVIN Carbonic anhydrase 2 OS=Bos taurus GN=CA2 PE=1 SV=3 * > P00489 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit5>* > sp|P00489|PYGM_RABIT Glycogen phosphorylase, muscle form OS=Oryctolagus > cuniculus GN=PYGM PE=1 SV=3 * P02769 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit6>* > sp|P02769|ALBU_BOVIN Serum albumin OS=Bos taurus GN=ALB PE=1 SV=4 * Q29443 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit7>* > sp|Q29443|TRFE_BOVIN Serotransferrin OS=Bos taurus GN=TF PE=2 SV=1 * P67975 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit8>* > sp|P67975|LACB_OVIMU Beta-lactoglobulin OS=Ovis orientalis musimon GN=LGB > PE=1 SV=1 * P79334 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit9>* > sp|P79334|PYGM_BOVIN Glycogen phosphorylase, muscle form OS=Bos taurus > GN=PYGM PE=1 SV=3 * P00922 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit10>* > sp|P00922|CAH2_SHEEP Carbonic anhydrase 2 OS=Ovis aries GN=CA2 PE=1 SV=2 * > P02662 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit11>* > sp|P02662|CASA1_BOVIN Alpha-S1-casein OS=Bos taurus GN=CSN1S1 PE=1 SV=2 * > P14639 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit12>* > sp|P14639|ALBU_SHEEP Serum albumin OS=Ovis aries GN=ALB PE=2 SV=1 * Q3B7M9 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit13>* > sp|Q3B7M9|PYGB_BOVIN Glycogen phosphorylase, brain form OS=Bos taurus > GN=PYGB PE=2 SV=3 * Q28554 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit14>* > sp|Q28554|G3P_SHEEP Glyceraldehyde-3-phosphate dehydrogenase (Fragment) > OS=Ovis aries GN=GAPDH PE=2 SV=4 * P49064 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit15>* > sp|P49064|ALBU_FELCA Serum albumin OS=Felis catus GN=ALB PE=1 SV=1 * P49822 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit16>* > sp|P49822|ALBU_CANFA Serum albumin OS=Canis familiaris GN=ALB PE=1 SV=3 * > P09571 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit17>* > sp|P09571|TRFE_PIG Serotransferrin OS=Sus scrofa GN=TF PE=1 SV=2 * P00432 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit18>* > sp|P00432|CATA_BOVIN Catalase OS=Bos taurus GN=CAT PE=1 SV=3 * P06278 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit19>* > sp|P06278|AMY_BACLI Alpha-amylase OS=Bacillus licheniformis GN=amyS PE=1 > SV=1 * A6YF56 > <http://www.apcf.edu.au/mascot/cgi/master_results.pl?file=E%3A%2Fdata%2F20110203%2FF143073.dat#Hit20>* > sp|A6YF56|ALBU_MESAU Serum albumin OS=Mesocricetus auratus GN=ALB PE=1 SV=1 > > > > -------------------------------------------------------------------------------------------------------------------------------------------------------------- > > > I am able to produce pepXML file and able to view results without any > issues, here is the output from the pepXML viewer screen. > > > --------------------------------------------------------------------------------------------------------------------- > *trypsin* digest, *MASCOT* search engine, quantitation: [none] > displaying * 2165 * of 2165 total spectra, page 1 of 44 > * 2135 unique peptides, * * 2132 unique stripped peptides, 2037 unique > proteins, 2012 single hits * > PepXML Viewer, 2006 SPC/ISB > > -------------------------------------------------------------------------------------------------------------------------------------------------------------- > > We are experincing difficulties in running PeptideProphet for the output > generated by Mascot search algorithm, I am here with enclosing the STDOUT > and STDERR messages generated by PeptideProphet run. > > ============================================== > STDOUT .... > ============================================== > Stdout of TPP for NEdwards-J2================================================= > > /home/APCF/tpp/bin/xinteract (TPP v4.4 JETSTREAM (unstable development > prerelease) rev 0, Build 201007011135 (linux)) > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser > 'NEdwards-J2.pepprophet.xml' 'NEdwards-J2.pep.xml' -L'7' -E'trypsin'" > > file 1: NEdwards-J2.pep.xml > > processed altogether 2165 results > > results written to file > /mnt/sanfs/APCF-PROD/results/tpp/2011-02-03/NEdwards-J2.pepprophet.shtml > > command completed in 1 sec > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser > 'NEdwards-J2.pepprophet.xml' DECOY='sp|decoy' MINPROB=0.05 EXTRAITRS=20 PI > RT" > > using pI > > using RT > > Using Decoy Label "sp|decoy". > > (MASCOT) > > results for charge 1: 37 id tot and 1 adj scores > > adding pI mixture distr > > adding Retention Time mixture distr > > results for charge 2: 1085 id tot and 38 adj scores > > results for charge 2: -7.19405 adj_ion_mean and 15.0557 adj_ion_hom mean > 62.9988id mean0.906181 correlation (r) > > 2+ ion - id = 0.965428*(ion - hom) + -21.7292 with error = 5.12625 > > mean ion - id: -7.19405, mean ion - hom: 15.0557 > > results for charge 3: 1043 id tot and 16 adj scores > > results for charge 4: 0 id tot and 0 adj scores > > results for charge 5: 0 id tot and 0 adj scores > > results for charge 6: 0 id tot and 0 adj scores > > results for charge 7: 0 id tot and 0 adj scores > > init with MASCOT trypsin > > MS Instrument info: Manufacturer: , Model: , Ionization: , Analyzer: , > Detector: > > Initialising statistical models ... > > Iterations: .........10.........20....Estimating Retention Time Model ... > please wait ... > > command "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser > 'NEdwards-J2.pepprophet.xml' DECOY='sp|decoy' MINPROB=0.05 EXTRAITRS=20 PI > RT" exited with non-zero exit code: 6 > > QUIT - the job is incomplete > > > ===================================================================================== > STDERR > > ===================================================================================== > Stderr of TPP for NEdwards-J2/bin/ln: creating symbolic link > `NEdwards-J2.mzXML' to `/home/APCF/uploads/2011-02-03/NEdwards-J2.mzXML': > File exists > > filepath: /mnt/sanfs/APCF-PROD/results/tpp/2011-02-03/, extn: NEdwards-J2 > > trypsin : cut(KR) nocuts(P) sense(C) > > prev_aa and next_aa have already been read from .dat file. > > Replacing 21537 protein id with full ids by parsing through the database... > > > searching > /mnt/sanfs/APCF/databases/SwissProt/decoy_uniprot_sprot_generic.fasta.....5%.....10%.....15%.....20%.....30%.....35%.....40%.....45%.....50%.....60%.....65%.....70%.....75%.....80%.....90%.....95%...done > > > PeptideProphet (TPP v4.4 JETSTREAM (unstable development prerelease) rev 0, > Build 201007011135 (linux)) AKeller@ISB > > read in 32 1+, 1081 2+, 1038 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. > > Found 956 Decoys, and 1195 Non-Decoys > > PeptideProphetParser: > Validation/InterProphet/InterProphetParser/KDModel.cxx:143: bool > KDModel::replaceProb(int, double): Assertion `idx < posprobs_->size()' > failed. > > ==================================================================== > > I wonder whether anyone has any idea about this error. > > > with regards, > > -- > Dr. Jagan Kommineni > Systems Administrator and Duty Programmer > Australian Proteomics Computational Facility > Ludwig Institute for Cancer Research, > 6th Floor, Royal Melbourne Hospital, > Royal Parade, Parkville, Victoria > Ph:03 9341-3177. > > -- > 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 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