I performed GATK to call variants. but got this error:
[April 13, 2019 5:24:50 AM CST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 567.92 minutes.
Runtime.totalMemory()=157205135360
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:3332)
at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:137)
However,I set Xmx240G for java GATK mutect2, with is a real large memory. I also set tmp file, but still report "java.lang.OutOfMemoryError".
There are two ~35G bam1 and ~7.2G bam2 for input, and reference about ~6.5G, 560 thousand scaffolds, because of not well assembled.
[April 13, 2019 5:24:50 AM CST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 567.92 minutes.
Runtime.totalMemory()=157205135360
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:3332)
at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:137)
However,I set Xmx240G for java GATK mutect2, with is a real large memory. I also set tmp file, but still report "java.lang.OutOfMemoryError".
There are two ~35G bam1 and ~7.2G bam2 for input, and reference about ~6.5G, 560 thousand scaffolds, because of not well assembled.