GenotypeGVCFs report java.lang.OutOfMemoryError: Java heap space while call incremental imported GenomicsDB about gatk

[gokalpcelik]

Hi @LYOKOIIIYYR
You seem to set your heapsize to the maximum memory size that you have which we do not recommend. GenotypeGVCFs does not need that much memory if I can recall. Can you set the heapsize to a more moderate number such as 8gb or 12 gb and try that way?

[droazen]

Yes, it's important to realize that GenomicsDB is implemented in C (not Java), and so the memory allocated for GenomicsDB is whatever is NOT allocated to Java (ie., whatever is left over after -Xmx). So -Xmx should never claim all of the memory on the machine, and should leave enough free memory for GenomicsDB to use.

[LYOKOIIIYYR]

There is no problem on runing GenomicsDBImport , and @gokalpcelik I have already tried Xmx10G to Xmx 14G and get the same error.
I'm most curious about why running GenomicsDB GenotypeGVCFs directly with 400 samples on the same computational resources can succeed, while running incremental GenomicsDB GenotypeGVCFs with 200 + 200 samples fails.