Any reason you would see this other than Tandem search failed to generate results?
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. On Tue, Aug 13, 2013 at 11:41 AM, Rishika Bisaria <[email protected]>wrote: > 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. > > > -- 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.
