Hi Jagan, Yes, this is likely the source of the error. Thanks for tracking it down in the code. I will commit a fix to our svn repository.
Thanks, -David On Mon, Feb 14, 2011 at 8:59 PM, Jagan Kommineni <[email protected]>wrote: > Dear All, > > > Further investigation on this problem with the current version (TPP > TPP_4-4-1) reveals that whenever the script "ASAPCGIDisplay.cgi" is called > for OMSSA results from the web pointer of the protXML file (viewer) which > internally calling a function (getSearchResult) to fetch result which > returns NULL. > > > Here is the function that is called inside ASAPCGIDisplay.cgi. > > > nextresult = getSearchResult(search_result_tags, search_engine); > > > ----------------------------------------------------------------------------------------------------------------------------- > SearchResult* > ASAPRatioProteinCGIDisplayParser::getSearchResult(Array<Tag*>* tags, char* > engine) { > if(! strcasecmp(engine, "SEQUEST")) > return new SequestResult(tags); > if(! strcasecmp(engine, "MASCOT")) > return new MascotResult(tags); > if(! strcasecmp(engine, "COMET")) > return new CometResult(tags); > if(! strcasecmp(engine, "TANDEM")) > return new TandemResult(tags); > if(! strcasecmp(engine, "X! Tandem (k-score)")) > return new TandemResult(tags); > if(! strcasecmp(engine, "PHENYX")) > return new PhenyxResult(tags); > return NULL; > } > > -------------------------------------------------------------------------------------------------------------------------- > > I couldn't find OMSSA entry in this function. I wonder whether anyone has > any idea about it. > > > with regards, > > > Jagan kommineni > > > > > On Mon, Feb 7, 2011 at 1:25 PM, Jagan Kommineni <[email protected] > > wrote: > >> Dear All, >> >> I have generated mgf file from the mzXML file >> (OR20080317_S_SILAC-LH_1-1_01.mzXML) which is one of the input file used by >> TPP team while presenting TPP tutorials during HUPO 2010 conference. >> >> I run omssa search against it. >> >> Then I have used following parameters in running PeptideProphet and >> ProteinProphet with ASAPRatio >> >> In the “PeptideProphet Options” pane select to “Use accurate mass >> binning” >> >> In the “ASAPRatio Options” section . >> 1. “Labeled Residues” to K and R, >> 2. Then I set “m/z range to include in summation of peak:” to 0.05. >> 3. “Specified masses:” to M 147.035, K 136.10916 and R 166.10941. >> 4. Check box option “Use fixed scan range”. >> >> *I was able to run PeptideProphet and ProteinProphet without any error >> message on the screen, >> * >> >> ------------------------------------------------------------------------------------------------------------------------------------------------------------ >> xinteract Command Line*/home/APCF/tpp/bin/xinteract >> -Njagan-J1772.pepprophet.xml -eT -d'sp|decoy' -p0.05 -l7 -x20 -R -OAP >> -A-s-lRK-F-r0.05-mM147.035K136.10916R166.10941---- jagan-J1772.pep.xml >> *ProteinProphet >> Command Line*/home/APCF/tpp/bin/ProteinProphet jagan-J1772.pepprophet.xml >> jagan-J1772.prot.xml ASAP_PROPHET ; >> ------------------------------------------------------------- >> * >> *I am here with enclosing STDOUT and STDERR messages ...* >> >> ------------------------------------------------------------------------------------------------------------------------------------------------------ >> Stdout of TPP for jagan-J1772 >> >> Archive: /home/APCF/results/omssa/2011-01-31/jagan-J1771.zip >> >> inflating: ./jagan-J1771/jagan-J1771.omx >> >> Reading jagan-J1772.omx as XML >> >> /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 >> 'jagan-J1772.pepprophet.xml' 'jagan-J1772.pep.xml' -P -L'7' -E'trypsin'" >> >> file 1: jagan-J1772.pep.xml >> >> processed altogether 8138 results >> >> results written to file >> /mnt/sanfs/APCF-PROD/results/tpp/2011-01-31/jagan-J1772.pepprophet.shtml >> >> command completed in 6 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser >> 'jagan-J1772.pepprophet.xml' DECOY='sp|decoy' MINPROB=0.05 EXTRAITRS=20 >> ACCMASS NONPARAM" >> >> using Accurate Mass Bins >> >> Using Decoy Label "sp|decoy". >> >> Using non-parametric distributions >> >> (OMSSA) >> >> WARNING!! The discriminant function for OMSSA is not yet complete. It is >> presented here to help facilitate trial and discussion. Reliance on this >> code for publishable scientific results is not recommended. >> >> adding Accurate Mass mixture distr >> >> init with OMSSA trypsin >> >> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: >> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN >> >> Initialising statistical models ... >> >> Iterations: .........10.........20...... >> >> model complete after 27 iterations >> >> command completed in 12 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/ProphetModels.pl -i >> jagan-J1772.pepprophet.xml -d 'sp|decoy'" >> >> Analyzing jagan-J1772.pepprophet.xml ... >> >> Reading Accurate Mass Model model +1 ... >> >> Reading Accurate Mass Model model +2 ... >> >> Reading Accurate Mass Model model +3 ... >> >> Reading Accurate Mass Model model +4 ... >> >> Reading Accurate Mass Model model +5 ... >> >> Reading Accurate Mass Model model +6 ... >> >> Reading Accurate Mass Model model +7 ... >> >> Parsing search results >> "/mnt/sanfs/APCF-PROD/results/tpp/2011-01-31/jagan-J1772 (OMSSA)"... >> >> => Total of 1485 hits. >> >> command completed in 1 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/ASAPRatioPeptideParser >> 'jagan-J1772.pepprophet.xml' -s -lRK -F -r0.05 >> -mM147.035K136.10916R166.10941 - - - -" >> >> command completed in 63 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/DatabaseParser >> 'jagan-J1772.pepprophet.xml'" >> >> command completed in 0 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/RefreshParser >> 'jagan-J1772.pepprophet.xml' >> '/mnt/sanfs/APCF/databases/SwissProt/decoy_uniprot_sprot_generic.fasta'" >> >> - Searching the tree... >> >> - Linking duplicate entries... - Printing results... >> >> command completed in 19 sec >> >> running: "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I >> /mnt/sanfs/APCF-PROD/results/tpp/2011-01-31/jagan-J1772.pepprophet.xml" >> >> command completed in 1 sec >> >> /mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser >> 'jagan-J1772.pepprophet.xml' 'jagan-J1772.pep.xml' -P -L'7' -E'trypsin' 6 >> sec >> >> /mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser >> 'jagan-J1772.pepprophet.xml' DECOY='sp|decoy' MINPROB=0.05 EXTRAITRS=20 >> ACCMASS NONPARAM 12 sec >> >> /mnt/sanfs/APCF/APCF_WEB/tpp/bin/ProphetModels.pl -i >> jagan-J1772.pepprophet.xml -d 'sp|decoy' 1 sec >> >> /mnt/sanfs/APCF/APCF_WEB/tpp/bin/ASAPRatioPeptideParser >> 'jagan-J1772.pepprophet.xml' -s -lRK -F -r0.05 >> -mM147.035K136.10916R166.10941 - - - - 63 sec >> >> /mnt/sanfs/APCF/APCF_WEB/tpp/bin/DatabaseParser >> 'jagan-J1772.pepprophet.xml' >> >> /mnt/sanfs/APCF/APCF_WEB/tpp/bin/RefreshParser >> 'jagan-J1772.pepprophet.xml' >> '/mnt/sanfs/APCF/databases/SwissProt/decoy_uniprot_sprot_generic.fasta' 19 >> sec >> >> /mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I >> /mnt/sanfs/APCF-PROD/results/tpp/2011-01-31/jagan-J1772.pepprophet.xml 1 sec >> >> >> job completed in 102 sec >> >> ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the >> original Perl by A. Keller (TPP v4.4 JETSTREAM (unstable development >> prerelease) rev 0, Build 201006071455 (linux)) >> >> (xml input) (ASAPRatio) (report Protein Length) (using degen pep info) >> >> . . . reading in >> /mnt/sanfs/APCF-PROD/results/tpp/2011-01-31/jagan-J1772.pepprophet.xml. . . >> >> . . . read in 0 1+, 994 2+, 491 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with >> min prob 0.05 >> >> >> . . . importing ASAPRatio protein ratios . . . and pvalues . . . >> >> Analyzing jagan-J1772.prot.xml ... >> >> Stderr of TPP for jagan-J1772#script file generated by >> tpp-submit.pl. Created at Mon Jan 31 15:07:13 2011 >> >> # ----------This ia a OMSSA->Prophets Job---------- >> >> #step -1: try and change protections on apcf output files >> >> #step 0: update db with time of start of job running >> >> ssh search.apcf.edu.au /var/www/APCF_WEB/APCF/job-start.pl jagan-J1772 >> >> #step 1: cd to the result dir so we can see mzXML file >> >> cd /home/APCF/results/tpp/2011-01-31 >> >> /usr/bin/unzip /home/APCF/results/omssa/2011-01-31/jagan-J1771.zip >> jagan-J1771/jagan-J1771.omx -d .; >> >> /bin/mv jagan-J1771/jagan-J1771.omx .; >> >> /bin/rm -rf jagan-J1771 >> >> /bin/ln jagan-J1771.omx jagan-J1772.omx; >> >> /bin/ln: creating hard link `jagan-J1772.omx' to `jagan-J1771.omx': File >> exists >> >> /home/APCF/omssa-2.1.9.linux/omssa2pepXML -o jagan-J1772.pep.xml >> jagan-J1772.omx; >> >> # step 2: set the viewing for the input pepxml file >> >> echo '' >jagan-J1772.pep.shtml >> >> echo '' >>jagan-J1772.pep.shtml >> >> echo '' >> jagan-J1772.pep.shtml >> >> echo '' >> jagan-J1772.pep.shtml >> >> echo '' >> jagan-J1772.pep.shtml >> >> echo '' >> jagan-J1772.pep.shtml >> >> echo '' >> jagan-J1772.pep.shtml >> >> #step5: call peptideProphet >> >> /home/APCF/tpp/bin/xinteract -Njagan-J1772.pepprophet.xml -eT -d'sp|decoy' >> -p0.05 -l7 -x20 -R -OAP -A-s-lRK-F-r0.05-mM147.035K136.10916R166.10941---- >> jagan-J1772.pep.xml >> >> PeptideProphet (TPP v4.4 JETSTREAM (unstable development prerelease) rev >> 0, Build 201007011135 (linux)) AKeller@ISB >> >> read in 3 1+, 3624 2+, 4366 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. >> >> Found 2186 Decoys, and 5807 Non-Decoys >> >> WARNING: Mixture model quality test failed for charge (1+). >> >> WARNING: Mixture model quality test failed for charge (4+). >> >> WARNING: Mixture model quality test failed for charge (5+). >> >> WARNING: Mixture model quality test failed for charge (6+). >> >> WARNING: Mixture model quality test failed for charge (7+). >> >> Warning: empty y range [0:0], adjusting to [0:1] >> >> Warning: empty y range [0:0], adjusting to [0:1] >> >> plot "jagan-J1772.pepprophet_IPPROB.tsv" using 2:1 title "iProphet" with >> line lc 2 , x notitle with line lt 0 lc -1 >> >> ^ >> >> "jagan-J1772.pepprophet_IPPROB.gp", line 16: warning: Skipping data file >> with no valid points >> >> - Building Commentz-Walter keyword tree...#rm jagan-J1772.dat >> >> #step5A: call proteinProphet >> >> /home/APCF/tpp/bin/ProteinProphet jagan-J1772.pepprophet.xml >> jagan-J1772.prot.xml ASAP_PROPHET ; >> >> INFO: mu=8.22677e-07, db_size=733092553 >> >> /home/APCF/tpp/bin/ProtProphModels.pl -i jagan-J1772.prot.xml; >> >> ------------------------------------------------------------------------------------------------------------------------------------------------------. >> * >> I am able to view ASAPRatio from the pepXML file generated after running >> PeptideProphet without any issues.* >> >> >> >> *I am also able to view pvalue curve from the ProteinXML Viewer but when >> I click ASAPRatio pointer, I get an error message "error" without any >> details. >> >> I wonder whether anyone has any idea what is going on here. I am here with >> enclosing the snap-shot for your ready reference. >> * >> >> 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. >> >> > > > -- > 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 this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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