Hi David, Thank you for your reply. I got the SRF file after the search against database by SEQUEST and then converted it to SQT file. Then, I tried to use TPP to calculate protein probability from SQT files. I find a function "Sqt2XML" in TPP-4.4.1, so I converted my SQT file to pepXML and started peptideprophet. Then I got this error message. Do you mean that TPP cannot handle SRF or SQT files? then, What is Sqt2XML working for? My data file is very big (~300M), where could I upload it to you? Many thanks, Kinfai
On Jun 22, 10:37 am, David Shteynberg <[email protected]> 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 <[email protected]> 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 [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group > > athttp://groups.google.com/group/spctools-discuss?hl=en. -- 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.
