Unfortunately, there is not much helpful information here. Have you checked the output of *all* your PeptideProphet runs for errors?
1.) I suggest you try TPP 4.8.0 which fixes some bugs in 4.7.1 2.) Also try the following options: xinteract -Ninteract-$f.pep.xml -OAPd -p0 -dDECOY -PPM $f.tandem.pep.xml InterProphetParser THREADS=32 `\ls interact-*is280*.pep.xml` is280.interact.ipro.pep.xml If you can compress and post one of your failing datasets where I can download it and test where it is failing that would be helpful. -David On Fri, Sep 11, 2015 at 9:20 AM, Rachel <[email protected]> wrote: > Dear David, > > 1) Just to make it clear, my problem is, iprophet works on some subsets of > my 300 files, but does not work all subsets. My each subset has same no of > files. For those have segmentation errors, there are no outputs being > generated. > 2) My peptideprophet and iprophet setting is as follows, > xinteract -Ninteract-$f.pep.xml -OARPd -dDECOY -PPM $f.tandem.pep.xml > InterProphetParser THREADS=32 DECOY=DECOY MINPROB=0.9 `\ls > interact-*is280*.pep.xml` is280.interact.ipro.pep.xml > 3) iprophet error and peptideprophet output tail are also attached for > your information. > Hope it helps. > Rachel > > > > On Wednesday, July 22, 2015 at 3:00:11 PM UTC+8, Rachel wrote: > >> I tried to merge ~300 pepxml files using xinteract, it failed for the >> command line is too long. Can anyone tell what is maximum no of pepxml we >> can merge using xinteract? >> >> Thanks so much! >> >> Rachel >> > -- > 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/d/optout. > -- 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/d/optout.
