Thanks for your quick response. I've modified my command to /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 -OdP -ddecoy 206_pepxml.xml
(also tried without the -Od option). Unfortunately I still get the same error. I've checked my 206_pepxml.xml file .. and the decoys are named as follows protein="decoy_9817" Is it possible that the error is related to not having the raw spectra? Or should I not worry about that? Thanks for your help. On Nov 9, 11:06 am, David Shteynberg <dshteynb...@systemsbiology.org> wrote: > Phenyx search results can only be processed with the semi-parametric > modeling based on decoys. Judging from name of your database, it does > have decoys in there. Now you must tell PeptideProphet to use the > semi-parametric model with xinteract option -OP and the decoy tag that > all your decoy proteins begin with using xinteract flag e.g. -dDECOY > if all your decoys proteins begin with DECOY. You can also use option > -Od to have PeptideProphet assign non-zero probabilities to the decoy > hits. > > -David > > > > > > > > On Mon, Nov 8, 2010 at 2:36 PM, ira cooke <iraco...@googlemail.com> wrote: > > 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 > > athttp://groups.google.com/group/spctools-discuss?hl=en. -- 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.
