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haplotypecaller keeps crashing with OutOfMemory exception during -ERC GVCF mode
HC keeps crashing with java.lang.OutOfMemoryError for some samples not all of them during -ERC GVCF mode.
I tried 5 samples but only two of them crashed.
I've tried different heap sizes (like 8G, 16G) or even without heap size and different thread numbers (like 8, 2) in vain.
Can you recommend how to avoid this?
I use GATK version 3.6-0-g89b7209 and here is the example command I tried:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -nct 16 -R /home/thchung/Data/NGSLibrary/iGenome/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -I /home/thchung/Test/FLAM76/indel_realigned_recal.bam --dbsnp /home/thchung/Data/NGSLibrary/GATKBundle/dbsnp_138.hg19.vcf -stand_call_conf 20.0 -stand_emit_conf 20.0 -ERC GVCF -o /home/thchung/Test/Variant/FLAM76_haplotypecaller.g.vcf
The GATK generated log ends like this:
INFO 21:26:48,614 ProgressMeter - chr2:201130386 2.49267192E8 6.6 h 95.0 s 14.5% 45.2 h 38.6 h
INFO 21:31:44,791 ProgressMeter - chr2:201130388 2.49267192E8 6.7 h 96.0 s 14.5% 45.8 h 39.1 h
INFO 21:33:45,069 ProgressMeter - chr2:201130388 2.49267192E8 6.7 h 96.0 s 14.5% 46.0 h 39.3 h
INFO 21:41:38,830 ProgressMeter - chr2:201130464 2.49267192E8 6.8 h 98.0 s 14.5% 46.9 h 40.1 h
INFO 21:45:12,246 ProgressMeter - chr2:201130674 2.49267192E8 6.9 h 99.0 s 14.5% 47.3 h 40.5 h