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-discuss+unsubscr...@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/CAGJJY%3D9d3pqdh7nwwT_JUg5_Qjn%3DwRP4BxC9SCTKVu8w%3D5ZABA%40mail.gmail.com.
