Skip to content

Fix EncyclopeDIA out of memory with large FASTA files #3552

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
wants to merge 9 commits into from
Closed

Fix EncyclopeDIA out of memory with large FASTA files #3552

Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
7de1844
Remove 12GB memory cap for "ConvertFastaToPrositCSV" process.
Jul 7, 2025
d32b895
Fix out of memory in ConvertBLIBToLibrary
Jul 7, 2025
ef80582
Merge remote-tracking branch 'remotes/origin/master' into Skyline/wor…
Jul 7, 2025
0869daa
Fix incorrect memory request.
Jul 8, 2025
564593d
Merge remote-tracking branch 'remotes/origin/master' into Skyline/wor…
Jul 8, 2025
9e46fca
Merge remote-tracking branch 'remotes/origin/master' into Skyline/wor…
Jul 19, 2025
a4d6263
Revert change regarding edu.washington.gs.maccoss.encyclopedia.cli.Co…
nickshulman Jul 31, 2025
aa50223
Merge remote-tracking branch 'remotes/origin/master' into Skyline/wor…
nickshulman Jul 31, 2025
4f44386
Merge branch 'master' into Skyline/work/20250707_IncreaseConvertFasta…
nickshulman Aug 27, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion pwiz_tools/Skyline/Model/Lib/EncyclopeDiaHelpers.cs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -182,7 +182,7 @@ public static void ConvertKoinaOutputToDlib(string koinaBlibFilepath, string fas
if (!EnsureRequiredFilesDownloaded(FilesToDownload, progressMonitor))
throw new InvalidOperationException(Resources.EncyclopeDiaHelpers_ConvertFastaToKoinaInputCsv_could_not_find_EncyclopeDia);

long javaMaxHeapMB = Math.Min(12 * 1024L * 1024 * 1024, MemoryInfo.TotalBytes / 2) / 1024 / 1024;
long javaMaxHeapMB = MemoryInfo.TotalBytes / 2 / 1024 / 1024 ;
const string csvToLibraryClasspath = "edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary";

var pr = new ProcessRunner();
Expand Down