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.
