change -l flag in xinteract from -l7 to -l1 p0.05 -l7 -x20 -O
p0.05 -l1 -x20 -O can be done in Petunia by setting minimum number of amino acids from default 7 to 1 Ulrich On Jan 6, 2009, at 2:39 AM, dre wrote: > > 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 -~----------~----~----~----~------~----~------~--~---
