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10 months ago
analyst
▴
60
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
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.