If I start with SRF file, what could I do to run the peptideprophet? On Jun 22, 10:37 am, David Shteynberg <david.shteynb...@systemsbiology.org> wrote: > Hi Kinfai, > > The problem lies in the error message: > (mspire: ms-sequest > not recognizedspire: ms-sequest) > > We have not processed this sort of data yet. If you want to post your > file here we can adjust the TPP to deal with these files in the > future: > > http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_A... > > Thanks, > -David > > > > > > > > On Wed, Jun 22, 2011 at 12:00 AM, Kinfai Au <kinfa...@gmail.com> wrote: > > After converting SQT file to pep.xml file, I ran the following > > command: > > > xinteract -Ninteract.pep.xml -p0.05 -l7 -O test5.pep.xml > > > Then, it crashed in some step. Here is the error message. I spent days > > on it but the pipeline TPP still fails. Could anyone give me some > > help? > > ################################################################ > > > xinteract (TPP v4.4 VUVUZELA rev 1, Build 201106201323 (linux)) > > > running: "/home/stow/swtree/stow/TPP-4.4.1/bin/InteractParser > > 'interact.pep.xml' 'test5.pep.xml' -L'7'" > > file 1: test5.pep.xml > > processed altogether 41651 results > > > results written to file /home/kinfai/test5/interact.pep.shtml > > > command completed in 44 sec > > > running: "/home/stow/swtree/stow/TPP-4.4.1/bin/PeptideProphetParser > > 'interact.pep.xml' MINPROB=0.05" > > )(mspire: ms-sequest > > not recognizedspire: ms-sequest > > > command "/home/stow/swtree/stow/TPP-4.4.1/bin/PeptideProphetParser > > 'interact.pep.xml' MINPROB=0.05" exited with non-zero exit code: 256 > > QUIT - the job is incomplete > > > -- > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to spctools-discuss@googlegroups.com. > > To unsubscribe from this group, send email to > > spctools-discuss+unsubscr...@googlegroups.com. > > For more options, visit this group > > athttp://groups.google.com/group/spctools-discuss?hl=en.
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