The script works perfectly without any error! Thanks for your help. [image: image.png]
On Thu, Dec 3, 2020 at 6:43 AM 'David Shteynberg' via spctools-discuss < spctools-discuss@googlegroups.com> wrote: > Use Jimmy's solution until the next release. > > On Wed, Dec 2, 2020 at 11:41 AM Asif Ahmed <kh.asifahme...@gmail.com> > wrote: > >> 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. >> 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-5Cd%3D0KhT-4dStif%2B15gczTH-pxt_FQ1iSA-m-4s7nkQ%40mail.gmail.com >> <https://groups.google.com/d/msgid/spctools-discuss/CABV_oz-5Cd%3D0KhT-4dStif%2B15gczTH-pxt_FQ1iSA-m-4s7nkQ%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%3D8xJzicksxYT%3DjRQXbU7Hqq5u5dNxg5nmK_HspEJ%2BPTdg%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D8xJzicksxYT%3DjRQXbU7Hqq5u5dNxg5nmK_HspEJ%2BPTdg%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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