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 <[email protected]> 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 [email protected]. >> 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/22052f7c-d0d9-494e-8208-b49b29fb8321n%40googlegroups.com.
