After further investigation on this problem found that it taking enormous amounts of memory (RAM) for running "RefreshParser" which is part of the xinteract for the result file that was obtained from the previous step (DatabaseParser) which didn't have any valid data to view in pepXMLViewer.
The functionality of the RefreshParser is to go into database and find all proteins corresponding to identified peptides. But in this case there are no results in the results file produced in the previous step (DatabaseParser). I wonder whether there is a bug in xinteract to continue running all the steps eventhough there is a bug in any one of the prevoius steps "InteractParser, PeptideProphetParser, ProphetModels.pl and DatabaseParser, RefreshParser and PepXMLViewer.cgi". I am not sure whether there is a problem in the RAW data itself. Please note that if we set xinteract option -p to 0 then all the steps continue without any error message. We ran few other models successfully without any issues. with regards, Jagan Kommineni On Mar 1, 10:44 am, Jagan Kommineni <[email protected]> wrote: > Dear All, > > I am trying to run xinteract with the following command ... > > /home/APCF/tpp/bin/xinteract -Njagan-J2906.pepprophet.xml -p0.05 -l7 - > x20 -O jagan-J2906.pep.xml > > I cab able to view jagan-J2906.pep.xml with pepXMLViewer and > got 3209 unique peptides. > ============================================================================== > trypsin digest, MASCOT search engine, quantitation: [none] > displaying 3489 of 3489 total spectra, page 1 of 70 > 3209 unique peptides, 3209 unique stripped peptides, 3209 unique > proteins, 3089 single hits > PepXML Viewer, 2006 SPC/ISB > ============================================================================== > > Here is the output the xinteract execution .... > ================================= > [a...@apcf-hn3 2010-02-26]$ /home/APCF/tpp/bin/xinteract -Njagan- > J2906.pepprophet.xml -p0.05 -l7 -x20 -O jagan-J2906.pep.xml > > /home/APCF/tpp/bin/xinteract (TPP v4.3 JETSTREAM rev 1, Build > 200912151720 (linux)) > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser 'jagan- > J2906.pepprophet.xml' 'jagan-J2906.pep.xml' -L'7'" > file 1: jagan-J2906.pep.xml > processed altogether 3489 results > > results written to file /mnt/sanfs/APCF/results/tpp/2010-02-26/jagan- > J2906.pepprophet.shtml > > command completed in 1 sec > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser 'jagan- > J2906.pepprophet.xml' MINPROB=0.05 EXTRAITRS=20" > (MASCOT) > results for charge 1: 1797 id tot and 0 adj scores > results for charge 2: 1399 id tot and 0 adj scores > results for charge 3: 259 id tot and 0 adj scores > results for charge 4: 34 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: Thermo Scientific, Model: LTQ > Orbitrap, Ionization: NSI, Analyzer: FTMS, Detector: unknown > > PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200912151720 > (linux)) akel...@isb > read in 915 1+, 1372 2+, 247 3+, 34 4+, 0 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > Iterations: .........10.........20.... > WARNING: Mixture model quality test failed for charge (1+). > WARNING: Mixture model quality test failed for charge (2+). > WARNING: Mixture model quality test failed for charge (3+). > WARNING: Mixture model quality test failed for charge (4+). > model complete after 25 iterations > command completed in 0 sec > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/ProphetModels.pl -i jagan- > J2906.pepprophet.xml" > Analyzing jagan-J2906.pepprophet.xml ... > Parsing search results "/mnt/sanfs/APCF/results/tpp/2010-02-26/jagan- > J2906 (MASCOT)"... > => Total of 0 hits. > Could not find/open font when opening font "arial", using internal non- > scalable font > Warning: empty y range [0:0], adjusting to [0:1] > Could not find/open font when opening font "arial", using internal non- > scalable font > > plot "jagan-J2906.pepprophet_PPPROB.tsv" using 2:1 title > "PeptideProphet" with line lc 2 , x notitle with line lt 0 lc -1 > > ^ > "jagan-J2906.pepprophet_PPPROB.gp", line 16: warning: Skipping data > file with no valid points > Could not find/open font when opening font "arial", using internal non- > scalable font > > plot "jagan-J2906.pepprophet_IPPROB.tsv" using 2:1 title "iProphet" > with line lc 2 , x notitle with line lt 0 lc -1 > > ^ > "jagan-J2906.pepprophet_IPPROB.gp", line 16: warning: Skipping data > file with no valid points > command completed in 0 sec > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/DatabaseParser 'jagan- > J2906.pepprophet.xml'" > command completed in 0 sec > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/RefreshParser 'jagan- > J2906.pepprophet.xml' '/mnt/sanfs/APCF/mascot/default/sequence/ > LudwigNR/current/LudwigNR_Q409_generic_forward.fasta'" > - Building Commentz-Walter keyword tree... - Searching the tree... > - Linking duplicate entries... - Printing results... > > command completed in 69 sec > > running: "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I / > mnt/sanfs/APCF/results/tpp/2010-02-26/jagan-J2906.pepprophet.xml" > > command "/mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi -I /mnt/ > sanfs/APCF/results/tpp/2010-02-26/jagan-J2906.pepprophet.xml" exited > with non-zero exit code: 11 > QUIT - the job is incomplete > [a...@apcf-hn3 2010-02-26]$ > > ======================================================================== > Results xml file (jagan-J2906.pepprophet.xml) has been uploaded to the > server and can be accessed with the following web pointer ... > ---------------------------------------------------------------------------------------------------------------------------------------------------http://spctools-discuss.googlegroups.com/web/jagan-J2906.pepprophet.x... > -------------------------------------------------------------------------------------------------------------------------------------------------- > For your immediate reference sake, I am here with sending tail > contents of the result file (jagan-J2906.pepprophet.xml) .. > ============================================================================= > <search_summary base_name="/mnt/sanfs/APCF/results/tpp/2010-02-26/ > jagan-J2906" search_engine="MASCOT" precursor_mass_type="monoisotopic" > fragment_mass_type="monoisotopic" out_data_type="out" out_data=".tgz" > search_id="1"> > <search_database local_path="/mnt/sanfs/APCF/mascot/default/sequence/ > LudwigNR/current/LudwigNR_Q409_generic_forward.fasta" type="AA"/> > <enzymatic_search_constraint enzyme="trypsin" > max_num_internal_cleavages="1" min_number_termini="2"/> > <aminoacid_modification aminoacid="B" mass="114.534940" > massdiff="114.534940" variable="N"/> > <aminoacid_modification aminoacid="J" mass="0.000000" > massdiff="0.000000" variable="N"/> > <aminoacid_modification aminoacid="O" mass="0.000000" > massdiff="0.000000" variable="N"/> > <aminoacid_modification aminoacid="U" mass="150.953630" > massdiff="150.953630" variable="N"/> > <aminoacid_modification aminoacid="X" mass="111.000000" > massdiff="111.000000" variable="N"/> > <aminoacid_modification aminoacid="Z" mass="128.550590" > massdiff="128.550590" variable="N"/> > <parameter name="LICENSE" value="Licensed to: Australian Proteomics > Computational Facility, (64 processors)."/> > <parameter name="MP" value=""/> > <parameter name="NM" value=""/> > <parameter name="COM" value="Conversion of C:\Documents and Settings > \Jagan Kommineni\My Documents\APCF\temp\O080119-01.mzXML to mascot > generic"/> > <parameter name="IATOL" value=""/> > <parameter name="IA2TOL" value=""/> > <parameter name="IASTOL" value=""/> > <parameter name="IBTOL" value=""/> > <parameter name="IB2TOL" value=""/> > <parameter name="IBSTOL" value=""/> > <parameter name="IYTOL" value=""/> > <parameter name="IY2TOL" value=""/> > <parameter name="IYSTOL" value=""/> > <parameter name="SEG" value=""/> > <parameter name="SEGT" value=""/> > <parameter name="SEGTU" value=""/> > <parameter name="LTOL" value=""/> > <parameter name="TOL" value="1.2"/> > <parameter name="TOLU" value="Da"/> > <parameter name="ITH" value=""/> > <parameter name="ITOL" value="0.6"/> > <parameter name="ITOLU" value="Da"/> > <parameter name="PFA" value="1"/> > <parameter name="DB" value="LudwigNR"/> > <parameter name="MODS" value=""/> > <parameter name="MASS" value="Monoisotopic"/> > <parameter name="CLE" value="Trypsin"/> > <parameter name="FILE" value="jagan-J2907.mgf"/> > <parameter name="PEAK" value="AUTO"/> > <parameter name="QUE" value=""/> > <parameter name="TWO" value=""/> > <parameter name="SEARCH" value="MIS"/> > <parameter name="USERNAME" value=""/> > <parameter name="USEREMAIL" value=""/> > <parameter name="CHARGE" value="2+ and 3+"/> > <parameter name="INTERMEDIATE" value=""/> > <parameter name="REPORT" value="20"/> > <parameter name="OVERVIEW" value=""/> > <parameter name="FORMAT" value="Mascot generic"/> > <parameter name="FORMVER" value="1.01"/> > <parameter name="FRAG" value=""/> > <parameter name="IT_MODS" value=""/> > <parameter name="USER00" value=""/> > <parameter name="USER01" value=""/> > <parameter name="USER02" value=""/> > <parameter name="USER03" value=""/> > <parameter name="USER04" value=""/> > <parameter name="USER05" value=""/> > <parameter name="USER06" value=""/> > <parameter name="USER07" value=""/> > <parameter name="USER08" value=""/> > <parameter name="USER09" value=""/> > <parameter name="USER10" value=""/> > <parameter name="USER11" value=""/> > <parameter name="USER12" value=""/> > <parameter name="PRECURSOR" value=""/> > <parameter name="TAXONOMY" value="All entries"/> > <parameter name="ACCESSION" value=""/> > <parameter name="REPTYPE" value="peptide"/> > <parameter name="SUBCLUSTER" value="0"/> > <parameter name="ICAT" value=""/> > <parameter name="INSTRUMENT" value="Default"/> > <parameter name="ERRORTOLERANT" value=""/> > <parameter name="FRAMES" value=""/> > <parameter name="CUTOUT" value=""/> > <parameter name="USERID" value="1012"/> > <parameter name="QUANTITATION" value="None"/> > <parameter name="DECOY" value=""/> > <parameter name="PEP_ISOTOPE_ERROR" value="0"/> > <parameter name="RULES" value="1,2,5,6,8,9,13,14"/> > <parameter name="INTERNALS" value="0.0,700.0"/> > </search_summary> > <analysis_timestamp analysis="database_refresh" > time="2010-03-01T10:22:25" id="1"> > <database_refresh_timestamp database="/mnt/sanfs/APCF/mascot/default/ > sequence/LudwigNR/current/LudwigNR_Q409_generic_forward.fasta"/> > </analysis_timestamp> > <analysis_timestamp analysis="peptideprophet" > time="2010-03-01T10:22:25" id="1"/> > </msms_run_summary> > </msms_pipeline_analysis> > ------------------------------------------------------------------------------------------------------------------------------------------------------------ > It looks like the data relating spectrum_query, search_hit etc .. are > missing from the result file. > ============================================================================== > When run PepXMLViewer.cgi on commandline then the result is > Segmentation fault > --------------------------------------------------------------------------------------------------------------------------- > [a...@apcf-hn3 2010-02-26]$ /mnt/sanfs/APCF/APCF_WEB/tpp/cgi-bin/ > PepXMLViewer.cgi -I /mnt/sanfs/APCF/results/tpp/2010-02-26/jagan- > J2906.pepprophet.xml > Segmentation fault > ============================================================= > However when I run /home/APCF/tpp/bin/xinteract -Njagan- > J2906.pepprophet.xml -p0.05 -l7 -x20 -O jagan-J2906.pep.xml > I am able to produce and view the result file with PepXMLViewer .... > ========================================================================== > > Can anybody has any experience with this type of error message? > > I wonder whether there is any check to see pepXML file is suitable to > run Prophets such as PeptideProphet and proteinProphet. > > -------------------------------------------------------------------------------------------------------------------------------------------- > > with regards, > > Jagan Kommineni -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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