What is the maximum number of scafflods allowed at GATK in reference genome?

timnatgatktimnatgatk University of KentuckyMember

Hello, I am working with very fragmented and very large genome. Over 10000000 scaffolds!
Even with very small bam files run into error
ERROR MESSAGE: An error occurred because you did not provide enough memory to run this program. You can use the -Xmx argument
I have used -Xmx500g and memory usage hardly achieves 50g before it failed.

We are going to split the reference, but it would be very useful to know limitations. Thank you!

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