If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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