Hi Andreas, I think you are doing everything correctly. The soruce of the problem is here:
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+). PeptideProphet modeling seems to have failed on your most abundant charges. You can try to force the model fitting to see if the invalidation of the mixture model (PeptideProphet QC) was warranted, the xinteract option for this is -OF . I would not recommend using this option for anything other than double check invalidated mixture models. It is more likely that there is some problem with either the data the database or the search parameters that are causing this run to have very few positive IDs. -David On Fri, Sep 18, 2009 at 11:30 AM, Andreas Quandt <[email protected]> wrote: > 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", 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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