Hi everyone, I have been trying all morning to get the proteomic pipeline to work for me, but it keeps giving me the same error msgs. First I tried using Mascot's export option to directly save the database search results as a pepXML file so that I could start directly at step 5 of the TPP and proceed with the peptide and protein prophet analysis, but this produced an error. Then I tried to start at the beginning of the pipeline and everything worked perfectly until the peptide prophet step. When I add my 6 pepXML files to the step 5 and run peptide prophet without any additional settings, I get the same error as before, which goes as follows:
---------------------------------------------------------------------------------------------------------------------------------------------------------------- run_in c:/Inetpub/wwwroot/ISB/data; xinteract -Ninteract.pep.xml - p0.05 -l7 -x20 -O c:/Inetpub/wwwroot/ISB/data/QMIX1_01.pep.xml c:/ Inetpub/wwwroot/ISB/data/QMIX2_01.pep.xml c:/Inetpub/wwwroot/ISB/data/ QMIX3_01.pep.xml c:/Inetpub/wwwroot/ISB/data/QMIX4_01.pep.xml c:/ Inetpub/wwwroot/ISB/data/QMIX5_01.pep.xml c:/Inetpub/wwwroot/ISB/data/ QMIX6_01.pep.xml xinteract (TPP v4.1 JETSTREAM rev 1, Build 200811121809 (MinGW)) running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "c:/ Inetpub/wwwroot/ISB/data/QMIX1_01.pep.xml" "c:/Inetpub/wwwroot/ISB/ data/QMIX2_01.pep.xml" "c:/Inetpub/wwwroot/ISB/data/QMIX3_01.pep.xml" "c:/Inetpub/wwwroot/ISB/data/QMIX4_01.pep.xml" "c:/Inetpub/wwwroot/ISB/ data/QMIX5_01.pep.xml" "c:/Inetpub/wwwroot/ISB/data/QMIX6_01.pep.xml" - L"7"" file 1: c:/Inetpub/wwwroot/ISB/data/QMIX1_01.pep.xml file 2: c:/Inetpub/wwwroot/ISB/data/QMIX2_01.pep.xml file 3: c:/Inetpub/wwwroot/ISB/data/QMIX3_01.pep.xml file 4: c:/Inetpub/wwwroot/ISB/data/QMIX4_01.pep.xml file 5: c:/Inetpub/wwwroot/ISB/data/QMIX5_01.pep.xml file 6: c:/Inetpub/wwwroot/ISB/data/QMIX6_01.pep.xml processed altogether 15791 results results written to file c:/Inetpub/wwwroot/ISB/data/interact.pep.xml direct your browser to http://localhost/ISB/data/interact.pep.shtml command completed in 8 sec running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" MINPROB=0.05 EXTRAITRS=20" (MASCOT) results for charge 1: 0 id tot and 0 adj scores error: -1.0 ion score command "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" MINPROB=0.05 EXTRAITRS=20" failed: Operation not permitted command "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml" MINPROB=0.05 EXTRAITRS=20" exited with non-zero exit code: 1 QUIT - the job is incomplete Command FAILED ---------------------------------------------------------------------------------------------------------------------------------------------------------------- This still produces a interact.pep.xml file, but when I try to run protein prophet using this generated file, it fails and reports the following error: ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Output Files * c:/Inetpub/wwwroot/ISB/data/interact.prot.shtml (file not found: not created or deleted?) Command 1 [Tue Jan 6 11:38:09 2009] [ Show / Hide ] ProteinProphet c:/Inetpub/wwwroot/ISB/data/interact.pep.xml c:/ Inetpub/wwwroot/ISB/data/interact.prot.xml Command FAILED --------------------------------------------------------------------------------------------------------------------------------------------------------------- Any help would be 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 at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
