Skyline (64-bit) 24.1.0.199 (6a0775ef83)

System.IO.IOException: Error occurred running process.
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
	at gnu.trove.map.hash.TCharObjectHashMap.setUp(TCharObjectHashMap.java:143)
	at gnu.trove.impl.hash.THash.<init>(THash.java:137)
	at gnu.trove.impl.hash.THash.<init>(THash.java:104)
	at gnu.trove.impl.hash.TPrimitiveHash.<init>(TPrimitiveHash.java:68)
	at gnu.trove.impl.hash.TCharHash.<init>(TCharHash.java:65)
	at gnu.trove.map.hash.TCharObjectHashMap.<init>(TCharObjectHashMap.java:79)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie$TrieNode.<init>(PeptideTrie.java:72)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie$TrieNode.getOrCreate(PeptideTrie.java:93)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie.<init>(PeptideTrie.java:29)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie.<init>(PeptideTrie.java:15)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideAccessionMatchingTrie.<init>(PeptideAccessionMatchingTrie.java:11)
	at edu.washington.gs.maccoss.encyclopedia.filereaders.BlibFile.getCopyEntriesToLibrary(BlibFile.java:221)
	at edu.washington.gs.maccoss.encyclopedia.filereaders.BlibToLibraryConverter.convert(BlibToLibraryConverter.java:141)
	at edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary.convert(ConvertBLIBToLibrary.java:64)
	at edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary.main(ConvertBLIBToLibrary.java:28)

Command-line: C:\Users\giole\AppData\Local\Apps\2.0\74LJTP4N.20P\Z69JC5WL.Y6T\skyl..tion_9286511f3362df93_0018.0001_5aeb0e19d93199bf\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe  -Xmx6098M -cp "C:\Users\giole\AppData\Local\Apps\2.0\74LJTP4N.20P\Z69JC5WL.Y6T\skyl..tion_9286511f3362df93_0018.0001_5aeb0e19d93199bf\Tools\encyclopedia-2.12.30-executable.jar" edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary -Duser.language=en-US -Duser.region=US -i "C:\Users\giole\Documents\FASTA file\uniprotkb_human_reviewed_plusTrypsin_2024_09_11-z3_nce27-koina-ms2pip_2021_HCD-AlphaPept_rt_generic-EB631BA7683CBEEB296C1CCCD44396C.blib" -f "C:\Users\giole\Documents\FASTA file\uniprotkb_human_reviewed_plusTrypsin_2024_09_11.fasta" -o "C:\Users\giole\Documents\FASTA file\uniprotkb_human_reviewed_plusTrypsin_2024_09_11-z3_nce27-koina.dlib"
Working directory:  ---> System.IO.IOException: Error occurred running process.
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
	at gnu.trove.map.hash.TCharObjectHashMap.setUp(TCharObjectHashMap.java:143)
	at gnu.trove.impl.hash.THash.<init>(THash.java:137)
	at gnu.trove.impl.hash.THash.<init>(THash.java:104)
	at gnu.trove.impl.hash.TPrimitiveHash.<init>(TPrimitiveHash.java:68)
	at gnu.trove.impl.hash.TCharHash.<init>(TCharHash.java:65)
	at gnu.trove.map.hash.TCharObjectHashMap.<init>(TCharObjectHashMap.java:79)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie$TrieNode.<init>(PeptideTrie.java:72)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie$TrieNode.getOrCreate(PeptideTrie.java:93)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie.<init>(PeptideTrie.java:29)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie.<init>(PeptideTrie.java:15)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideAccessionMatchingTrie.<init>(PeptideAccessionMatchingTrie.java:11)
	at edu.washington.gs.maccoss.encyclopedia.filereaders.BlibFile.getCopyEntriesToLibrary(BlibFile.java:221)
	at edu.washington.gs.maccoss.encyclopedia.filereaders.BlibToLibraryConverter.convert(BlibToLibraryConverter.java:141)
	at edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary.convert(ConvertBLIBToLibrary.java:64)
	at edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary.main(ConvertBLIBToLibrary.java:28)

Command-line: C:\Users\giole\AppData\Local\Apps\2.0\74LJTP4N.20P\Z69JC5WL.Y6T\skyl..tion_9286511f3362df93_0018.0001_5aeb0e19d93199bf\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe  -Xmx6098M -cp "C:\Users\giole\AppData\Local\Apps\2.0\74LJTP4N.20P\Z69JC5WL.Y6T\skyl..tion_9286511f3362df93_0018.0001_5aeb0e19d93199bf\Tools\encyclopedia-2.12.30-executable.jar" edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary -Duser.language=en-US -Duser.region=US -i "C:\Users\giole\Documents\FASTA file\uniprotkb_human_reviewed_plusTrypsin_2024_09_11-z3_nce27-koina-ms2pip_2021_HCD-AlphaPept_rt_generic-EB631BA7683CBEEB296C1CCCD44396C.blib" -f "C:\Users\giole\Documents\FASTA file\uniprotkb_human_reviewed_plusTrypsin_2024_09_11.fasta" -o "C:\Users\giole\Documents\FASTA file\uniprotkb_human_reviewed_plusTrypsin_2024_09_11-z3_nce27-koina.dlib"
Working directory: 

Output:
[22:21:30] Indexing uniprotkb_human_reviewed_plusTrypsin_2024_09_11-z3_nce27-koina-ms2pip_2021_HCD-AlphaPept_rt_generic-EB631BA7683CBEEB296C1CCCD44396C.blib ...
[22:21:35] Reading BLIB file
[22:21:40] Starting alignment 1 with 2478817 data points
[22:22:43] Reading Fasta file uniprotkb_human_reviewed_plusTrypsin_2024_09_11.fasta
[22:22:43] Reading standard formated FASTA database
[22:22:43] Constructing trie from library peptides
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
	at gnu.trove.map.hash.TCharObjectHashMap.setUp(TCharObjectHashMap.java:143)
	at gnu.trove.impl.hash.THash.<init>(THash.java:137)
	at gnu.trove.impl.hash.THash.<init>(THash.java:104)
	at gnu.trove.impl.hash.TPrimitiveHash.<init>(TPrimitiveHash.java:68)
	at gnu.trove.impl.hash.TCharHash.<init>(TCharHash.java:65)
	at gnu.trove.map.hash.TCharObjectHashMap.<init>(TCharObjectHashMap.java:79)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie$TrieNode.<init>(PeptideTrie.java:72)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie$TrieNode.getOrCreate(PeptideTrie.java:93)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie.<init>(PeptideTrie.java:29)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie.<init>(PeptideTrie.java:15)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideAccessionMatchingTrie.<init>(PeptideAccessionMatchingTrie.java:11)
	at edu.washington.gs.maccoss.encyclopedia.filereaders.BlibFile.getCopyEntriesToLibrary(BlibFile.java:221)
	at edu.washington.gs.maccoss.encyclopedia.filereaders.BlibToLibraryConverter.convert(BlibToLibraryConverter.java:141)
	at edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary.convert(ConvertBLIBToLibrary.java:64)
	at edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary.main(ConvertBLIBToLibrary.java:28)

 ---> System.IO.IOException: Error occurred running process.
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
	at gnu.trove.map.hash.TCharObjectHashMap.setUp(TCharObjectHashMap.java:143)
	at gnu.trove.impl.hash.THash.<init>(THash.java:137)
	at gnu.trove.impl.hash.THash.<init>(THash.java:104)
	at gnu.trove.impl.hash.TPrimitiveHash.<init>(TPrimitiveHash.java:68)
	at gnu.trove.impl.hash.TCharHash.<init>(TCharHash.java:65)
	at gnu.trove.map.hash.TCharObjectHashMap.<init>(TCharObjectHashMap.java:79)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie$TrieNode.<init>(PeptideTrie.java:72)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie$TrieNode.getOrCreate(PeptideTrie.java:93)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie.<init>(PeptideTrie.java:29)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideTrie.<init>(PeptideTrie.java:15)
	at edu.washington.gs.maccoss.encyclopedia.datastructures.PeptideAccessionMatchingTrie.<init>(PeptideAccessionMatchingTrie.java:11)
	at edu.washington.gs.maccoss.encyclopedia.filereaders.BlibFile.getCopyEntriesToLibrary(BlibFile.java:221)
	at edu.washington.gs.maccoss.encyclopedia.filereaders.BlibToLibraryConverter.convert(BlibToLibraryConverter.java:141)
	at edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary.convert(ConvertBLIBToLibrary.java:64)
	at edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary.main(ConvertBLIBToLibrary.java:28)

Command-line: C:\Users\giole\AppData\Local\Apps\2.0\74LJTP4N.20P\Z69JC5WL.Y6T\skyl..tion_9286511f3362df93_0018.0001_5aeb0e19d93199bf\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe  -Xmx6098M -cp "C:\Users\giole\AppData\Local\Apps\2.0\74LJTP4N.20P\Z69JC5WL.Y6T\skyl..tion_9286511f3362df93_0018.0001_5aeb0e19d93199bf\Tools\encyclopedia-2.12.30-executable.jar" edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary -Duser.language=en-US -Duser.region=US -i "C:\Users\giole\Documents\FASTA file\uniprotkb_human_reviewed_plusTrypsin_2024_09_11-z3_nce27-koina-ms2pip_2021_HCD-AlphaPept_rt_generic-EB631BA7683CBEEB296C1CCCD44396C.blib" -f "C:\Users\giole\Documents\FASTA file\uniprotkb_human_reviewed_plusTrypsin_2024_09_11.fasta" -o "C:\Users\giole\Documents\FASTA file\uniprotkb_human_reviewed_plusTrypsin_2024_09_11-z3_nce27-koina.dlib"
Working directory: 
   in pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\skyline_24_1\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:riga 203
   --- Fine della traccia dello stack dell'eccezione interna ---
   --- Fine della traccia dello stack dell'eccezione interna ---
   in pwiz.Common.SystemUtil.ProcessRunner.ThrowExceptionWithOutput(Exception exception, String output) in C:\proj\skyline_24_1\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:riga 263
   in pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\skyline_24_1\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:riga 245
   in pwiz.Skyline.Model.Lib.EncyclopeDiaHelpers.ConvertKoinaOutputToDlib(String koinaBlibFilepath, String fastaFilepath, String encyclopeDiaDlibFilepath, IProgressMonitor progressMonitor, IProgressStatus& status) in C:\proj\skyline_24_1\pwiz_tools\Skyline\Model\Lib\EncyclopeDiaHelpers.cs:riga 205
   in pwiz.Skyline.FileUI.PeptideSearch.EncyclopeDiaSearchControl.Search(EncyclopeDiaSettings settings, CancellationTokenSource token, IProgressStatus status) in C:\proj\skyline_24_1\pwiz_tools\Skyline\FileUI\PeptideSearch\EncyclopeDiaSearchDlg.cs:riga 712