Will, Thanks for the update!
Cheers, David On Thu, Apr 15, 2021, 6:22 AM Will Comstock <wc...@cornell.edu> wrote: > Hi David, > > An update just in case anyone else has run into our issue: I copied the > PTMProphetParser.exe from a 6.0.0 installation over into our current 5.2.0 > installation, and everything is working great thus far! > > Thank you for the tip, I appreciate the assistance. > > Respectfully, > -Will > > On Tuesday, March 16, 2021 at 8:46:35 PM UTC-4 David Shteynberg wrote: > >> Hi Will, >> >> There is a release candidate for version 6.0.0 available on sourceforge: >> >> https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v6.0%20%28Release%20Candidates%29/ >> >> If you do end up trying it let me know if you find any issues. >> >> Thanks! >> -David >> >> On Tue, Mar 16, 2021 at 5:14 PM Will Comstock <wc...@cornell.edu> wrote: >> >>> Hi David, >>> >>> I'll attempt to re-run PTMProphet analysis on a few problematic datasets >>> with MAXTHREADS=1. >>> >>> I am currently using the version of PTMProphet that came with the >>> installation of TPP 5.2. Is there a newer version available that I could be >>> using instead? >>> >>> Thanks for your help! >>> -Will >>> >>> On Tuesday, March 16, 2021 at 7:37:58 PM UTC-4 David Shteynberg wrote: >>> >>>> Hello Will, >>>> >>>> We routinely run PTMProphet on datasets containing multiple hundreds of >>>> thousands of PSMs. This looks like multithreading issue >>>> related MAXTHREADS=0 parameter, this should not happen if you use >>>> MAXTHREADS=1. I have corrected several bugs related to multithreading in >>>> the codebase. Which version of PTMProphet are you using? >>>> >>>> Thanks, >>>> -David >>>> >>>> On Tue, Mar 16, 2021 at 3:59 PM Will Comstock <wc...@cornell.edu> >>>> wrote: >>>> >>>>> Hey everyone, >>>>> >>>>> I've run into an issue with PTMProphet where occasionally the command >>>>> will fail for unknown reasons and the resulting ptm.pep.xml cannot be >>>>> opened with the PepXML viewer. The command log seems to cut off abruptly, >>>>> as pictured in the attached screenshot. Also attached is the page that >>>>> appears upon trying to open the ptm.pep.xml. >>>>> >>>>> The interact.pep.xml files we're analyzing clock in at about 200 to >>>>> 250 megabytes. As a workaround, we currently just split the initial batch >>>>> of pep.xmls into smaller groups before running PeptideProphet and >>>>> PTMProphet on them again. Sometimes we end up with batches of pep.xmls as >>>>> small as 3 or 4 files, which is somewhat inconvenient for projects with >>>>> hundreds of RAW files. >>>>> >>>>> Is there another way around this issue? We've tried running it through >>>>> the command line as well and this problem still crops up frequently. >>>>> [image: PTMproph_CommandFailed.png] >>>>> [image: PTMproph_CommandFailed_xmlError.png] >>>>> Thanks! >>>>> >>>>> -- >>>>> 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-discu...@googlegroups.com. >>>>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/spctools-discuss/020c5be3-14ad-4350-9b12-dbb366fdb2c8n%40googlegroups.com >>>>> <https://groups.google.com/d/msgid/spctools-discuss/020c5be3-14ad-4350-9b12-dbb366fdb2c8n%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-discu...@googlegroups.com. >>> >> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/spctools-discuss/22052f7c-d0d9-494e-8208-b49b29fb8321n%40googlegroups.com >>> <https://groups.google.com/d/msgid/spctools-discuss/22052f7c-d0d9-494e-8208-b49b29fb8321n%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/b5eceb74-1e34-4c71-9f09-27b1e266ec89n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/b5eceb74-1e34-4c71-9f09-27b1e266ec89n%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/CAGJJY%3D-ABEbtJqMzKrjkRkmJpsooY%2BApx8pqUFyRtnJCnOvSoQ%40mail.gmail.com.
