Normally PeptideProphet errors out when it detects that the instrument names are not identical as it expects the statistical models from data generated on different instruments to be different and therefore not suitable for building a single model for both types of data. This error can be turned into a warning using the -Ow flag for xinteract, for Petunia users this flag should be written in the box titled "Enter additional options to pass directly to the command-line (expert use only!) "
-David On Sat, Jan 11, 2014 at 12:30 PM, Adrian Guthals <[email protected]>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 [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. > -- 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.
