Use Jimmy's solution until the next release. On Wed, Dec 2, 2020 at 11:41 AM Asif Ahmed <[email protected]> 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 < > [email protected]> 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 <[email protected]> >> 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 < >>> [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 >>> <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 >> [email protected]. >> 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:* [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-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 the Google Groups "spctools-discuss" group. 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