Maldi option for PeptideProphet always segfaults
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sirlark
Aug 10, 2012, 4:54:59 AM8/10/12
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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
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
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