Stick with Comet 2019.01.5. In version 2020.01.0, I deprecated the "deltacnstar" score in Comet and it looks like PeptideProphet can't run w/o it. Alternately, run this Perl command on your pep.xml files before running PeptideProphet if you want a workaround with the latest Comet:
perl -i -pe 's/<search_score name="deltacn"/<search_score name="deltacnstar" value="0.0"\/>\n <search_score name="deltacn"/g;' yourfile.pep.xml On Wed, Dec 2, 2020 at 10:27 AM Asif Ahmed <[email protected]> wrote: > Hi, > > I did a comet search (Comet version "2020.01 rev. 0") in Linux HPC, update > the paths of .mzML files, but when I tried to combine and run > peptide-prophet (on TPP v5.2.0), I am getting this error. I tried to > combine all the files, without running peptide-prophet and it works! > > Can you please advice me- what to do? > > ASIF > > > > > -- > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/2537e476-9ae1-45c4-974d-c087a337c667n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/2537e476-9ae1-45c4-974d-c087a337c667n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAJqD6EN9s1Dbiu1eSkcq64A4%3DG_T_%3DRoqeyqgR98iGJcR9u04g%40mail.gmail.com.
