hi brian, many thanks for looking into it! i also tried to process the file with different options but always the same error. it would be awesome if you (or natalie) could test the uploaded files (andreasquandt_090918.zip) as i otherwise do not know how to solve this problem :-(.
cheers, andreas On Fri, Sep 18, 2009 at 7:20 PM, Brian Pratt <[email protected]>wrote: > 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 > <[email protected]>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: [email protected] >> >> >> >> >> --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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