Hi, Thank you for the reply. Actually I want to follow this pipeline: Tandem->peptideprophet->q3new->proteinprophet->Q3proteinRatioParser.
And also when I am using Xinteract , I am getting the below error: running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.iproph.pep.xml" Analyzing interact.iproph.pep.xml ... Reading NSS model ... Reading NRS model ... Reading NSE model ... Reading NSI model ... Reading NSM model ... Reading NSP model ... Parsing search results "SP062512_062912_IP0201_AX01_23to24 (X! Tandem (k-score))"... => Total of 0 hits. => Total of 0 decoy hits. => Total of 0 excluded hits. command completed in 1 sec running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/xtandem/interact.iproph.pep.xml" command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/xtandem/interact.iproph.pep.xml" failed: Unknown error command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I c:/xtandem/interact.iproph.pep.xml" exited with non-zero exit code: -1073741819 QUIT - the job is incomplete On Tue, Aug 13, 2013 at 2:28 PM, David Shteynberg < [email protected]> wrote: > 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 a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/W_HCVBI82aM/unsubscribe > . > To unsubscribe from this group and all its topics, 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.
