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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.
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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
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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
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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.