Hi, I am trying to run the TPP pipeline with an XTandem search followed by significance testing by PeptideProphet+iProphet (all default parameters for high/low CID MS/MS with non-specific enzyme cleavage). The first issue I observed was that something in the TPP pipeline was truncating the .tandem result files while they were being converted to pepXML - I got around this by converting the .tandem files with "Tandem2XML" via command line just after the initial search. Now I get this error when trying to run PeptideProphet+iProphet on the *.pep.xml files. I am running release 4.5.2 installed from source on ubuntu x64. Here is the log output from the webserver page:
file 53: 011309_yeastLysC_F2_DTree2.2014_01_08_22_05_51.t.tandem.pep.xml file 54: 011309_yeastLysC_F3_DTree2.2014_01_08_22_08_22.t.tandem.pep.xml file 55: 011309_yeastLysC_F4_DTree2.2014_01_08_22_11_19.t.tandem.pep.xml file 56: 011309_yeastLysC_F5_DTree2.2014_01_08_22_13_22.t.tandem.pep.xml file 57: 011309_yeastLysC_F6_DTree2.2014_01_08_22_14_33.t.tandem.pep.xml file 58: 011309_yeastLysC_F7_DTree2.2014_01_08_22_15_35.t.tandem.pep.xml file 59: 011309_yeastLysC_F8_DTree2.2014_01_08_22_16_26.t.tandem.pep.xml file 60: 011309_yeastLysC_F9_DTree2.2014_01_08_22_17_06.t.tandem.pep.xml processed altogether 389175 results results written to file /usr/local/tpp/data/coon_swaney10_rep2_smallDB/interact-interact.pep.shtml command completed in 29 sec running: "/usr/local/tpp/bin/DatabaseParser 'interact-interact.pep.xml'" command completed in 0 sec running: "/usr/local/tpp/bin/RefreshParser 'interact-interact.pep.xml' '/usr/local/tpp/data/coon_swaney10_rep2_smallDB/uniprot-yeast-reference.fasta'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 23 sec running: "/usr/local/tpp/bin/PeptideProphetParser 'interact-interact.pep.xml' MINPROB=0.01 ACCMASS" using Accurate Mass Bins (X! Tandem) adding Accurate Mass mixture distr init with X! Tandem nonspecific ERROR: two instrument models: LTQ Orbitrap XL and LTQ Orbitrap command "/usr/local/tpp/bin/PeptideProphetParser 'interact-interact.pep.xml' MINPROB=0.01 ACCMASS" exited with non-zero exit code: 256 QUIT - the job is incomplete END OUTPUT RETURN CODE:256 ###### End Command Execution ###### # All finished at Sat Jan 11 12:10:53 2014 # END COMMAND BLOCK -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
