PTMProphet command failure (for larger datasets?)

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Will Comstock

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Mar 16, 2021, 6:59:00 PMMar 16
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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.
PTMproph_CommandFailed.png
PTMproph_CommandFailed_xmlError.png
Thanks!

David Shteynberg

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Mar 16, 2021, 7:37:58 PMMar 16
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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

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Will Comstock

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Mar 16, 2021, 8:14:22 PMMar 16
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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

David Shteynberg

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Mar 16, 2021, 8:46:35 PMMar 16
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Hi Will,

There is a release candidate for version 6.0.0 available on sourceforge:

If you do end up trying it let me know if you find any issues. 

Thanks!
-David

Will Comstock

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Apr 15, 2021, 9:22:46 AMApr 15
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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

David Shteynberg

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Apr 15, 2021, 12:21:31 PMApr 15
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Will,

Thanks for the update! 

Cheers, 
David

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