Are you building the TPP from source? All the code is here: https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/ but if building from SVN source is too much headache we should have an official release coming up in the next few weeks give or take. Meanwhile, Jimmy's solution will also have the same result.
On Wed, Dec 2, 2020 at 11:23 AM Asif Ahmed <kh.asifahme...@gmail.com> wrote: > 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 < > spctools-discuss@googlegroups.com> 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 <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 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 >> 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 >> <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:* khandakerasif.ah...@csiro.au; > khandaker-asif.ah...@students.mq.edu.au. > *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 spctools-discuss+unsubscr...@googlegroups.com. > 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 > <https://groups.google.com/d/msgid/spctools-discuss/CABV_oz_%2BJin1n0WVdCrb%2BiqfPUj3Op5%3DiDH4SVgPq4KHabB%3D4Q%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%3D9Wz-z4BA1ujQrHik801_o%2BUibbdYJasFpp5OCxoU7Uyw%40mail.gmail.com.
