You pipeline is missing the InteractParser step. Once you have a pep.xml file from Tandem you can run "xinteract -ip -p0 "on it to generate InteractParser->PeptideProphet->iProphet->ProteinProphet pipeline results.
-David On Tue, Aug 13, 2013 at 10:16 AM, Rishika Bisaria <[email protected]>wrote: > Hi, > I am able to run successfully the TPP pipeline on one of the mzXML > file.But on using TPP on other mzXML file , ProteinProphet is throwing > error stating that did you forgot to run PeptideProphet. > I have crossed checked all the parameters , they are correct.I am using > the latest version of TPP on windows and running it using commandline. > > 1.tandem input.xml > 2.Tandem2XML output.2013_07_24_13_24_28.t.xml > output.2013_07_24_13_24_28.pep.xml > 3.PeptideProphetParser output.2013_07_24_13_24_28.pep.xml MINPROB=0.2 > 4.ProteinProphet output.2013_07_24_13_24_28.pep.xml > c:\Inetpub\wwwroot\out1.prot.xml > > **** > > P.S. Everytime I am changing the parameters in input.xml file.I am using > k-score function. > > > Thanks, > Rishika > > -- > 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.
