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Java heap size error after Haplotypecaller finished traversal
This is strange and I am not sure if it has affected my gvcf file in any way or not, but I got the java heap size error after the traversal got over:
02:05:31.559 INFO ProgressMeter - Traversal complete. Processed 18934916 total regions in 22931.7 minutes.
02:05:49.823 INFO HaplotypeCaller - Shutting down engine
[13 March 2018 02:05:49 GMT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 22,932.27 minutes.
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
When I checked the gvcf file of some similar samples where Haplotypecaller finished successfully, the start and end bin of gvcf of the last call was same, and hence I came to know that the run was succesful in this case. But, is there any chance there may be some other error of some sort that I may be unaware? I gave 4 GB to my java and I am running GATK 188.8.131.52.