My guess is its nothing you're doing wrong - iProphet is still pretty new and it's probably confusing the PepXMLViewer parser. If you can upload the file that crashed pepXMLViewer to ftp://insilicos.serveftp.net/pub I Natalie or I will be happy to have a look.
Brian On Fri, Sep 18, 2009 at 6:47 AM, Andreas Quandt <quandt.andr...@gmail.com>wrote: > dear list, > > > when running following command (tpp 4.3.1) > > /usr/local/apps/tpp/bin/xinteract > -N/IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml -dDECOY_ -OAlIwp > /IMSB/results/workflow/45/Tandem2PepXML_/O08-10105_c.mzXML.pep.xml > > > i get following error: > > > --------------------------------------------- > /usr/local/apps/tpp/bin/xinteract (TPP v4.3 JETSTREAM rev 1, Build > 200909181208 (linux)) > > running: "/usr/local/apps/tpp/bin/InteractParser > '/IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml' > '/IMSB/results/workflow/45/Tandem2PepXML_/O08-10105_c.mzXML.pep.xml' -L'7'" > file 1: /IMSB/results/workflow/45/Tandem2PepXML_/O08-10105_c.mzXML.pep.xml > processed altogether 1290 results > > > results written to file > /IMSB/results/workflow/45/Xinteract_/Xinteract.pep.shtml > > > > command completed in 0 sec > running: "/usr/local/apps/tpp/bin/PeptideProphetParser > '/IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml' DECOY=DECOY_ > ACCMASS LEAVE PI INSTRWARN" > using Accurate Mass Bins > using pI > Using no error on different instrument types. > Using Decoy Label "DECOY_". > (X! Tandem) > WARNING: Found unanticipated cleavage in refinement mode. Turning off NTT > model. > adding Accurate Mass mixture distr > adding pI mixture distr > init with X! Tandem trypsin MS Instrument info: Manufacturer: > ThermoFinnigan, Model: LTQ Orbitrap XL, Ionization: ESI, Analyzer: ITMS, > Detector: EMT > > PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909181208 (linux)) > akel...@isb > read in 0 1+, 1135 2+, 137 3+, 18 4+, 0 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > Iterations: .........10.........20....... > WARNING: Mixture model quality test failed for charge (2+). > WARNING: Mixture model quality test failed for charge (3+). > model complete after 28 iterations > command completed in 1 sec > running: "/usr/local/apps/tpp/bin/ProphetModels.pl -i > /IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml" > Analyzing /IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml ... > Reading Accurate Mass Model model +1 ... > Reading kernel density calc pI [pI] model +1 ... > Reading Accurate Mass Model model +2 ... > Reading kernel density calc pI [pI] model +2 ... > Reading Accurate Mass Model model +3 ... > Reading kernel density calc pI [pI] model +3 ... > Reading Accurate Mass Model model +4 ... > Reading kernel density calc pI [pI] model +4 ... > Reading Accurate Mass Model model +5 ... > Reading kernel density calc pI [pI] model +5 ... > Reading Accurate Mass Model model +6 ... > Reading kernel density calc pI [pI] model +6 ... > Reading Accurate Mass Model model +7 ... > Reading kernel density calc pI [pI] model +7 ... > Parsing search results "/IMSB/scratch/andreas/O08-10105_c (X! Tandem)"... > => Total of 0 hits. > Warning: empty y range [0:0], adjusting to [0:1] > Warning: empty y range [0:0], adjusting to [0:1] > > plot "/IMSB/results/workflow/45/Xinteract_/Xinteract.pep_PPPROB.tsv" using > 2:1 title "PeptideProphet" with line lc 2 , x notitle with line lt 0 lc -1 > > > ^ > "/IMSB/results/workflow/45/Xinteract_/Xinteract.pep_PPPROB.gp<http://xinteract.pep_ppprob.gp/>", > line 16: warning: Skipping data file with no valid points > > plot "/IMSB/results/workflow/45/Xinteract_/Xinteract.pep_IPPROB.tsv" using > 2:1 title "iProphet" with line lc 2 , x notitle with line lt 0 lc -1 > > ^ > "/IMSB/results/workflow/45/Xinteract_/Xinteract.pep_IPPROB.gp<http://xinteract.pep_ipprob.gp/>", > line 16: warning: Skipping data file with no valid points > command completed in 0 sec > running: "/usr/local/apps/tpp/bin/DatabaseParser > '/IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml'" > command completed in 0 sec > running: "/usr/local/apps/tpp/bin/RefreshParser > '/IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml' > '/IMSB/data/databases/uniprot/sp_9606.fasta'" > - Building Commentz-Walter keyword tree... - Searching the tree... > - Linking duplicate entries... - Printing results... > > command completed in 1 sec > running: "/usr/local/apps/tpp/cgi-bin/PepXMLViewer.cgi -I > /IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml" > Segmentation fault > > command "/usr/local/apps/tpp/cgi-bin/PepXMLViewer.cgi -I > /IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml" exited with non-zero > exit code: 35584 > QUIT - the job is incomplete > --------------------------------------- > > > can someone explain me what the error code means and what i am doing wrong? > > > p.s. > > i played a little bit around with the parameter but get always the same > error message. > i also checked the output of the xtandem run (contains over 1000 valid > models) and also the pep.xml (which is valid). > > > > > -- > Andreas Quandt, PhD > Institute of Molecular Systems Biology > Swiss Federal Institute of Technology Zurich (ETH) > Wolfgang-Pauli-Str. 16 > ETH Hönggerberg, HPT D 76 > CH-8093 Zürich > > Tel: +41 44 633 3449 > Fax: +41 44 633 1051 > Mobil:+41 78 899 5206 E-mail: qua...@imsb.biol.ethz.ch > > > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
