Hi, Are you able to put some of this data somewhere? I'm currently looking another segfault so have a debug install to run through with a debugger. Would happily look at this MALDI data problem as it's something we might want to deal with in the near future.
DT On Friday, August 10, 2012 3:54:59 AM UTC-5, sirlark wrote: > > Hi, > > I'm running maldi data from an Applied Biosystems 4800, exported by the > manufacturer's conversion tool to mzML, then converted to mzXML using > proteowizards msconvert. When performing a peptide analysis (on any of the > 8 data sets I have available) if I select "Maldi data" in the > PeptideProphet options, I always get a segfault. I've installed TPP (4.5r2) > from source as per the wiki guide (which I wrote during the process). I > paste the log below. > > Thanks, > James > > # Commands for session 84G9DWEAK on Wed Aug 8 19:29:31 2012 > # BEGIN COMMAND BLOCK > ###### BEGIN Command Execution ###### > [Wed Aug 8 19:29:31 2012] EXECUTING: cd > /usr/local/tpp/data/0128_MASS_USSH_BIO-M; /usr/local/tpp/bin/xinteract > -Ninteract_itraq8plex_113denom.pep.xml -p0.05 -l7 -Omp -dDECOY > -Lcondition_itraq8plex_113denom.xml-1 > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_100-150mM_run_1.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_10mM_run_1.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_10mM_run_2.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_1mM_run_2.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_1mM_run_3.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_20mM_run_1.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_20mM_run_2.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_2mM_run_1.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_2mM_run_2.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_2mM_run_3.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_35mM_run_1.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_35mM_run_2.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_500-strip_SCX1-2mM_run_1.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_50mM_run_1.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_50mM_run_2.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_5mM_run_1.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_5mM_run_2.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_5mM_run_3.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_5mM_run_4.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_75mM_run_1.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_75mM_run_2.tandem.pep.xml > 0128_MASS_USSF_BIO-M_S_Hatting_SCX_5mM_run_1.tandem.pep.xml > OUTPUT: > > /usr/local/tpp/bin/xinteract (TPP v4.5 RAPTURE rev 2, Build 201202071404 > (linux)) > > running: "/usr/local/tpp/bin/InteractParser > 'interact_itraq8plex_113denom.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_100-150mM_run_1.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_10mM_run_1.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_10mM_run_2.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_1mM_run_2.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_1mM_run_3.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_20mM_run_1.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_20mM_run_2.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_2mM_run_1.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_2mM_run_2.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_2mM_run_3.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_35mM_run_1.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_35mM_run_2.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_500-strip_SCX1-2mM_run_1.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_50mM_run_1.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_50mM_run_2.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_5mM_run_1.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_5mM_run_2.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_5mM_run_3.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_5mM_run_4.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_75mM_run_1.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SAX_75mM_run_2.tandem.pep.xml' > '0128_MASS_USSF_BIO-M_S_Hatting_SCX_5mM_run_1.tandem.pep.xml' -L'7'" > file 1: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_100-150mM_run_1.tandem.pep.xml > file 2: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_10mM_run_1.tandem.pep.xml > file 3: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_10mM_run_2.tandem.pep.xml > file 4: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_1mM_run_2.tandem.pep.xml > file 5: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_1mM_run_3.tandem.pep.xml > file 6: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_20mM_run_1.tandem.pep.xml > file 7: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_20mM_run_2.tandem.pep.xml > file 8: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_2mM_run_1.tandem.pep.xml > file 9: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_2mM_run_2.tandem.pep.xml > file 10: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_2mM_run_3.tandem.pep.xml > file 11: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_35mM_run_1.tandem.pep.xml > file 12: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_35mM_run_2.tandem.pep.xml > file 13: > 0128_MASS_USSF_BIO-M_S_Hatting_SAX_500-strip_SCX1-2mM_run_1.tandem.pep.xml > file 14: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_50mM_run_1.tandem.pep.xml > file 15: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_50mM_run_2.tandem.pep.xml > file 16: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_5mM_run_1.tandem.pep.xml > file 17: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_5mM_run_2.tandem.pep.xml > file 18: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_5mM_run_3.tandem.pep.xml > file 19: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_5mM_run_4.tandem.pep.xml > file 20: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_75mM_run_1.tandem.pep.xml > file 21: 0128_MASS_USSF_BIO-M_S_Hatting_SAX_75mM_run_2.tandem.pep.xml > file 22: 0128_MASS_USSF_BIO-M_S_Hatting_SCX_5mM_run_1.tandem.pep.xml > processed altogether 16461 results > > > results written to file > /usr/local/tpp/data/0128_MASS_USSH_BIO-M/interact_itraq8plex_113denom.pep.shtml > > > > command completed in 3 sec > > running: "/usr/local/tpp/bin/DatabaseParser > 'interact_itraq8plex_113denom.pep.xml'" > command completed in 0 sec > > running: "/usr/local/tpp/bin/RefreshParser > 'interact_itraq8plex_113denom.pep.xml' > '/usr/local/tpp/data/dbase/sequence_dbs/uniprot_Rattus_ratus_contaminants_DECOY.fasta'" > - Building Commentz-Walter keyword tree... - Searching the tree... > - Linking duplicate entries... - Printing results... > > command completed in 3 sec > > running: "/usr/local/tpp/bin/PeptideProphetParser > 'interact_itraq8plex_113denom.pep.xml' MINPROB=0.05 MALDI DECOY=DECOY" > maldi mode > Using Decoy Label "DECOY". > (X! Tandem (k-score)) > init with X! Tandem (k-score) trypsin > MS Instrument info: Manufacturer: Applied Biosystems, Model: 4800 Proteomics > Analyzer, Ionization: matrix-assisted laser desorption ionization, Analyzer: > time-of-flight, Detector: microchannel plate detector > > PeptideProphet (TPP v4.5 RAPTURE rev 2, Build 201202071404 (linux)) > AKeller@ISB > read in 16445 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. > Segmentation fault > > command "/usr/local/tpp/bin/PeptideProphetParser > 'interact_itraq8plex_113denom.pep.xml' MINPROB=0.05 MALDI DECOY=DECOY" exited > with non-zero exit code: 35584 > QUIT - the job is incomplete > END OUTPUT > RETURN CODE:35584 > ###### End Command Execution ###### > # All finished at Wed Aug 8 19:29:38 2012 > # END COMMAND BLOCK > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/HevkSxvnuE4J. 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