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Memory error - Downsampling unavailable (3.5
I am working on mitochondrial genomes (250 samples) with a coverage of ~7000x.
The HC (v 3.5) is running perfectly for the firsts 248 samples but reaching the last ones, the following Java error appears :
##### 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.
All the other samples work perfectly with ~64G of mem and v_mem so i tried 128G but it is still not sufficient for my last samples to be processed. As you probably understand, i can't extend the memory indefinitely and I would want to know if it exists a way to force the down-sampling or at least to greatly ameliorate the memory used by the HaplotypeCaller.
Thanks for your time,