In the input .mzXML files I found both "<msModel category="msModel" value="LTQ Orbitrap"/>" and "<msModel category="msModel" value="LTQ Orbitrap XL"/>". I replaced 'LTQ Orbitrap XL' with 'LTQ Orbitrap' in all input files and I am re-running the pipeline now, hopefully this will fix the issue.
On Saturday, January 11, 2014 12:30:41 PM UTC-8, Adrian Guthals wrote: > > 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
