It would be helpful to see all of the output from the latest command. You might have to unravel the pipeline and run the steps separately if the Phenyx pepXML is missing some information. Would it be possible for you post you Phenyx pepXML file and the database so I can try it in a debugger?
Thanks, -David On Mon, Nov 8, 2010 at 6:19 PM, ira cooke <[email protected]> wrote: > 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 <[email protected]> > 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 <[email protected]> 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 [email protected]. >> > To unsubscribe from this group, send email to >> > [email protected]. >> > 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 [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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