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java out of memory error through beagle for imputation

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

beagle imputation java
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updated by Ram Ram • written by Bushra Bibi Bushra Bibi

1 answer

Resolved by increasing heapsize of -Xmx50G

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written by Bushra Bibi Bushra Bibi

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.

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written by Ruwaa • Ruwaa

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