I am using the windows version, any suggestion for that? On Thu, 3 Dec 2020 at 6:30 am, 'David Shteynberg' via spctools-discuss < spctools-discuss@googlegroups.com> wrote:
> 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 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%3D9Wz-z4BA1ujQrHik801_o%2BUibbdYJasFpp5OCxoU7Uyw%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D9Wz-z4BA1ujQrHik801_o%2BUibbdYJasFpp5OCxoU7Uyw%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. 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