Hi, I've been struggling to run PeptideProphet on phenyx generated pepXML files.
The error I get from PeptideProphet is "read in no data". Full output from the tool is as follows; ------------------ <BEGIN COMMANDLINE OUTPUT>----------------- /usr/local/tpp-4-4-0/bin/xinteract -Ninteract.pep.xml -p0 -eT -l7 -D/ var/www/ISB/data/Databases/OnMascot/SPHuman/ sphuman_20101013_DECOY.fasta 206_pepxml.xml /usr/local/tpp-4-4-0/bin/xinteract (TPP v4.4 VUVUZELA rev 0, Build 201010010955 (linux)) running: "/usr/local/tpp-4-4-0/bin/InteractParser 'interact.pep.xml' '206_pepxml.xml' -D'/var/www/ISB/data/Databases/OnMascot/SPHuman/ sphuman_20101013_DECOY.fasta' -L'7' -E'trypsin'" file 1: 206_pepxml.xml processed altogether 182 results results written to file /var/www/ISB/data/Projects/TRegs/SP/Phenyx/ interact.pep.shtml command completed in 3 sec running: "/usr/local/tpp-4-4-0/bin/PeptideProphetParser 'interact.pep.xml' MINPROB=0" (PHENYX) (minprob 0) WARNING!! The discriminant function for Phenyx is not yet complete. It is presented here to help facilitate trial and discussion. Reliance on this code for publishable scientific results is not recommended. init with PHENYX trypsin MS Instrument info: Manufacturer: ThermoFinnigan, Model: default, Ionization: FIXME, Analyzer: FIXME, Detector: FIXME PeptideProphet (TPP v4.4 VUVUZELA rev 0, Build 201010010955 (linux)) akel...@isb read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. read in no data command "/usr/local/tpp-4-4-0/bin/PeptideProphetParser 'interact.pep.xml' MINPROB=0" exited with non-zero exit code: 256 QUIT - the job is incomplete ------------------ <END COMMANDLINE OUTPUT>----------------- Note that without the -eT option I get a crash (segmentation fault). The enzyme specified inside the phenyx pepXML is <sample_enzyme name="Trypsin_(KR_noP)"> </sample_enzyme> (to be honest I'm not sure if this means trypsin or stricttrypsin ... but that's probably another issue as I get the error with -eS option as well). Could this error be caused by a lack of raw data files? I ran the phenyx searches on another computer and the file contains paths to raw data on that computer. I did try fixing the paths (and copying the raw data to a TPP accessible location) ... but that didn't work either. I guess my question is what does "read in no data" mean? Does data refer to the original spectra, or does it refer to something in the output of InteractParser (ie interact.pep.xml). Any help at all on this issue would be much appreciated Thanks -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
