Error code 139 when searching with "No enzyme"

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Nate Camp

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May 22, 2024, 9:43:20 AMMay 22
to Comet ms/ms db search support
Hi Jimmy,

I'm trying to search with enzyme set to none, and when I run the prophets I am getting error code 139 (see attached pic). After a quick google search I don't really understand what this error means. Perhaps this has something to do with our HPC settings? I figured I'd check you first before running it by our IT department. I've also attached my params file in case something is fishy there.

Thanks for the help!


exit_code_139.PNG
comet.params

Nate Camp

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May 22, 2024, 10:25:03 AMMay 22
to Comet ms/ms db search support
Forgot to mention - everything runs fine when i run a standard trypsin search.

Jimmy Eng

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May 22, 2024, 12:36:06 PMMay 22
to Comet ms/ms db search support
Nate, can you send me that "20210720***100ng.pep.xml"?  Either in an email or via file share.  The hard part with this is that if you're going to need a software update to Comet or the TPP to address this issue, that's going to be painful based on everything we just went through/learned with central computing at your org. 

Jimmy

Jimmy Eng

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May 22, 2024, 6:23:14 PMMay 22
to Comet ms/ms db search support
Just to give some closure to this thread if anyone comes across this issue in the future, this issue was due to a bug present in Comet in the 2017 thru 2018 releases that was addressed in release 2018.01.2.  The bug manifests itself as corrupted masses in the pep.xml output when there is a static modification and no variable modifications specified in the search.  Using a newer versions of Comet would address this issue as it was identified and fixed back in 2018.
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