Thanks Jimmy, i will try your suggestion. It took a while to generate the pep.xml files, So I would prefer your perl script.
David, is it possible to share the link? i was going to source forge website, but could not find it. On Thu, 3 Dec 2020 at 5:58 am, 'David Shteynberg' via spctools-discuss < [email protected]> wrote: > 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 <[email protected]> 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 <[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 >> <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 a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/TXNSCJwoGuU/unsubscribe > . > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D8XDEEXaGUGV8cWaeeHwNNB3SeAeGCaR6mygF-FB_mR-w%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D8XDEEXaGUGV8cWaeeHwNNB3SeAeGCaR6mygF-FB_mR-w%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- *Khandaker Asif Ahmed* PhD Student| Applied BioSciences, Macquarie University, NSW, Australia Postgraduate Research Student| CSIRO Land and Water Flagship, Black Mountain, ACT, Australia *Address:* Room No: S1.03, Building No: 101, CSIRO Clunies Ross Street, Black Mountain, ACT 2601, Australia *Alternative Email:* [email protected]; [email protected]. *Mobile:* (+61)0434018803, *Skype ID:* kh.asifratul Linkedin <https://www.linkedin.com/in/khandaker-asif-ahmed-24b461115/> | ResearchGate <https://www.researchgate.net/profile/Khandaker_Asif_Ahmed> | Google Scholar <https://scholar.google.com.au/citations?user=rUJ9DVAAAAAJ&hl=en> -- 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/CABV_oz_%2BJin1n0WVdCrb%2BiqfPUj3Op5%3DiDH4SVgPq4KHabB%3D4Q%40mail.gmail.com.
