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.
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