java.lang.OutOfMemoryError: Java heap space

[AdilyAid]

Hello,

I run abra2.22 as part of cwl pipeline of nucleo.
abra2 runs for few days and than crashed:

INFO	Fri Sep 09 09:01:34 UTC 2022	PROCESS_REGION_MSECS:	chr9_5391847_5392563	802613	0	1834	0
INFO	Fri Sep 09 09:01:40 UTC 2022	PROCESS_REGION_MSECS:	chr9_5394500_5394751	27	0	6	0
INFO	Fri Sep 09 09:01:44 UTC 2022	PROCESS_REGION_MSECS:	chr9_5395989_5396107	21	0	0	0
INFO	Fri Sep 09 09:01:53 UTC 2022	PROCESS_REGION_MSECS:	chr9_5402364_5402613	8967	0	1	0
INFO	Fri Sep 09 09:01:58 UTC 2022	PROCESS_REGION_MSECS:	chr9_5403925_5404129	5748	0	1	0
INFO	Fri Sep 09 09:03:56 UTC 2022	PROCESS_REGION_MSECS:	chr9_5404631_5405449	117556	5	109	0
INFO	Fri Sep 09 09:04:10 UTC 2022	PROCESS_REGION_MSECS:	chr9_5405647_5406088	14397	1	19	0
INFO	Fri Sep 09 09:04:47 UTC 2022	PROCESS_REGION_MSECS:	chr9_5406273_5406759	36378	0	44	0
INFO	Fri Sep 09 09:04:52 UTC 2022	PROCESS_REGION_MSECS:	chr9_5414156_5414311	5786	0	4	0
INFO	Fri Sep 09 09:04:59 UTC 2022	PROCESS_REGION_MSECS:	chr9_5418517_5418643	6388	0	2	0
INFO	Fri Sep 09 09:04:59 UTC 2022	PROCESS_REGION_MSECS:	chr9_5418888_5419047	27	0	3	0
INFO	Fri Sep 09 09:20:44 UTC 2022	chr10:43114788 : 	Curr reads size: 575009
INFO	Fri Sep 09 10:00:55 UTC 2022	chr1:156874308 : 	Curr reads size: 554415
INFO	Fri Sep 09 10:25:22 UTC 2022	chr4:1808187 : 	Curr reads size: 408300
INFO	Fri Sep 09 11:20:25 UTC 2022	chr6:117321312 : 	Curr reads size: 618944
INFO	Fri Sep 09 12:42:03 UTC 2022	PROCESS_REGION_MSECS:	chr9_5420197_5421057	1331503	1	2437	0
INFO	Fri Sep 09 12:42:08 UTC 2022	PROCESS_REGION_MSECS:	chr9_5421423_5421585	5741	0	1	0
INFO	Fri Sep 09 12:42:14 UTC 2022	PROCESS_REGION_MSECS:	chr9_5422622_5422717	5211	0	1	0
INFO	Fri Sep 09 12:52:30 UTC 2022	chr1:156874311 : 	Curr reads size: 556194
INFO	Fri Sep 09 15:12:08 UTC 2022	chr1:156874314 : 	Curr reads size: 558110
INFO	Fri Sep 09 17:33:53 UTC 2022	chr6:117321315 : 	Curr reads size: 619345
INFO	Fri Sep 09 18:16:03 UTC 2022	PROCESS_REGION_MSECS:	chr2_29222739_29223539	3495717	1	3989	0
INFO	Fri Sep 09 19:09:00 UTC 2022	chr1:156874318 : 	Curr reads size: 559856
INFO	Fri Sep 09 19:16:38 UTC 2022	chr14:104773477 : 	Curr reads size: 542026
java.lang.OutOfMemoryError: Java heap space
	at java.lang.String.<init>(String.java:325)
	at htsjdk.samtools.util.StringUtil.bytesToString(StringUtil.java:301)
	at htsjdk.samtools.util.StringUtil.bytesToString(StringUtil.java:288)
	at htsjdk.samtools.BinaryTagCodec.readNullTerminatedString(BinaryTagCodec.java:423)
	at htsjdk.samtools.BinaryTagCodec.readSingleValue(BinaryTagCodec.java:318)
	at htsjdk.samtools.BinaryTagCodec.readTags(BinaryTagCodec.java:282)
	at htsjdk.samtools.BAMRecord.decodeAttributes(BAMRecord.java:313)
	at htsjdk.samtools.BAMRecord.getAttribute(BAMRecord.java:293)
	at htsjdk.samtools.SAMRecord.getAttribute(SAMRecord.java:1110)
	at htsjdk.samtools.SAMRecord.getStringAttribute(SAMRecord.java:1220)
	at abra.SortedSAMWriter.addAlignment(SortedSAMWriter.java:104)
	at abra.ReAligner.remapReads(ReAligner.java:779)
	at abra.ReAligner.processChromosomeChunk(ReAligner.java:424)
	at abra.ReAlignerRunnable.go(ReAlignerRunnable.java:21)
	at abra.AbraRunnable.run(AbraRunnable.java:20)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
java.lang.OutOfMemoryError: Java heap space
	at abra.SimpleMapper.getPositionMismatches(SimpleMapper.java:80)
	at abra.SimpleMapper.map(SimpleMapper.java:157)
	at abra.ReadEvaluator.getImprovedAlignment(ReadEvaluator.java:70)
	at abra.ReadEvaluator.getImprovedAlignment(ReadEvaluator.java:34)
	at abra.ReAligner.remapRead(ReAligner.java:592)
	at abra.ReAligner.remapReads(ReAligner.java:771)
	at abra.ReAligner.processChromosomeChunk(ReAligner.java:424)
	at abra.ReAlignerRunnable.go(ReAlignerRunnable.java:21)
	at abra.AbraRunnable.run(AbraRunnable.java:20)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
INFO [job abra2_2_22] Max memory used: 24762MiB

When I it run on a small input it finished successfully. But for bigger fastq files - 6 GB - it was very slow and didn't finished.
The command is:
/usr/src/abra2-2.22.jar --threads 16 --tmpdir /tmp --cons --ca 10,1 --in gatk_uncollapsed_MD.bam --mad 1000 --mmr 0.1 --no-edge-ci --nosort --out UBG_abra2_uncollapsed_IR.bam --ref hg38.fasta --sga 8,32,48,1 --sc 100,30,80,15 --targets gatk_uncollapsed_MD.bed --ws 800,700

What can be the reason for using so many memory and why each step by interval took so long?

Thank you in advance for your help,
Adily

[colindaven]

You seem to be missing the -Xmx parameter in your command, try -Xmx32g.

See this example for 16g

java -Xmx16G -jar abra2.jar --in normal.bam,tumor.bam --out normal.abra.bam,tumor.abra.bam --ref hg38.fa --threads 8 --targets targets.bed --tmpdir /your/tmpdir > abra.log