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/-/xuBjghXI3EwJ. 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