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", 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", 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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