java out of memory error through beagle for imputation

Question

[analyst]

I am running beagle for imputation using following command:

   java -jar ~/Downloads/beagle.28Jun21.220.jar gt=merged_filtered_sorted_snps.vcf out=merged_snps_imputed.vcf nthreads=80

But got following error:

Window 5 [NC_068558.1:554-40000445] Reference markers:
401,104 Study markers: 401,104 java.lang.OutOfMemoryError: Java heap space java.lang.OutOfMemoryError: Java heap space java.lang.OutOfMemoryError: Java heap space

Answer 1

[analyst]

Resolved by increasing heapsize of -Xmx50G

[Ruwaa]

Mine was solved by increasing the heap space to 100GB -Xmx100G (50 GB didn't solve my issue).

I think this depends on the size of your vcf file but there's no guide yet on how much space you need to allocate.