I have updated PeptideProphetParser so that it CAN run with the new version of Comet. You will have to get it from the TPP SVN repository.
On Wed, Dec 2, 2020 at 10:50 AM Jimmy Eng <jke...@gmail.com> wrote: > 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 <kh.asifahme...@gmail.com> > 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 spctools-discuss+unsubscr...@googlegroups.com. >> 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 spctools-discuss+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/CAJqD6EN9s1Dbiu1eSkcq64A4%3DG_T_%3DRoqeyqgR98iGJcR9u04g%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAJqD6EN9s1Dbiu1eSkcq64A4%3DG_T_%3DRoqeyqgR98iGJcR9u04g%40mail.gmail.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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D8XDEEXaGUGV8cWaeeHwNNB3SeAeGCaR6mygF-FB_mR-w%40mail.gmail.com.
