Fix EncyclopeDIA out of memory with large FASTA files #3552
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added 6 commits
July 7, 2025 11:07
Fixed out of memory error running EncyclopeDIA on large FASTA files (reported by Giovanni, Shay, and John)
…k/20250707_IncreaseConvertFastaToKoinaInputCsvMemoryLimit
…k/20250707_IncreaseConvertFastaToKoinaInputCsvMemoryLimit
…k/20250707_IncreaseConvertFastaToKoinaInputCsvMemoryLimit
…nvertFastaToPrositCSV.
…k/20250707_IncreaseConvertFastaToKoinaInputCsvMemoryLimit
…ToKoinaInputCsvMemoryLimit
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I think this is unnecessary with my "Search Tools" PR. The default max Java heap for all tools will be 2/3 of total memory, but users can change it if they wish. |
I figured that would probably end up being true, but I wonder if we should commit this fix now anyway so that if anyone else runs into this problem can point them to Skyline-daily even before PR #3587 is committed. |
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Closing because this will eventually be made irrelevant by PR #3587 |
nickshulman
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Skyline/work/20250707_IncreaseConvertFastaToKoinaInputCsvMemoryLimit
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Fixed out of memory error running EncyclopeDIA with large FASTA files (reported by Shay and John)
This change removes the arbitrary 4GB or 12GB limit when running EncyclopeDIA's "ConvertFastaToPrositCSV" and "ConvertBLIBToLibrary", and, instead, use up to half of total memory.
Users would sometimes run out of memory with large FASTA files or high number of max missed cleavages.
https://skyline.ms/announcements/home/support/thread.view?rowId=69507