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haplotypecaller keeps crashing with OutOfMemory exception during -ERC GVCF mode

thchungthchung SingaporeMember


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

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.6-0-g89b7209):
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://www.broadinstitute.org/gatk
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: An error occurred because you did not provide enough memory to run this program. You can use the -Xmx argument (before the -jar argument) to adjust the maximum heap size provided to Java. Note that this is a JVM argument, not a GATK argument.
ERROR ------------------------------------------------------------------------------------------


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