FarmGeek4Life
commented
2 years ago There is not a flag for it, but MSGF+ checks if those helper files exist (and does some integrity checks on them), and if they are good, it just uses them, rather than recreating them.
From: Florian Christoph Sigloch @.> Sent: Monday, February 28, 2022 4:14:16 AM To: MSGFPlus/msgfplus @.> Cc: Subscribed @.***> Subject: [MSGFPlus/msgfplus] Use already existing database help files (Issue #134)
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Describe the question or problem Can MSGF+ be sped up by reusing already existing database help files, when re-analyzing or analyzing several files with the same database?
Details When running MSGF+, the first step is the suffix creation and sorting of the used database file. This creates four help files (.canno, .clncp, .csarr, cseq) and a database concatenated with decoys. For larger databases, this is a time-consuming step. I often analyze a bunch of raw data sequentially, using always the same database. For every raw file, these database help files are created from scratch.
Isn't it possible to re-use the files created earlier? Maybe it is not always wanted behavior, but could you create an additional parameter for MSGF+ that allows to re-use already existing database help files? This would speed up a lot of my analyses quite a bit.
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Describe the question or problem Can MSGF+ be sped up by reusing already existing database help files, when re-analyzing or analyzing several files with the same database?
Details When running MSGF+, the first step is the suffix creation and sorting of the used database file. This creates four help files (.canno, .clncp, .csarr, cseq) and a database concatenated with decoys. For larger databases, this is a time-consuming step. I often analyze a bunch of raw data sequentially, using always the same database. For every raw file, these database help files are created from scratch.
Isn't it possible to re-use the files created earlier? Maybe it is not always wanted behavior, but could you create an additional parameter for MSGF+ that allows to re-use already existing database help files? This would speed up a lot of my analyses quite a bit.