kc
New Member
Posts: 9
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Post by kc on Feb 26, 2014 2:52:20 GMT
Hi there,
I'm trying out the estimation the GRM following the tutorial. There are about ~900K SNPs and 10,000 individuals in my samples and the command I used is:
./gcta64 --bfile sample --autosome --maf 0.01 --grm-bin test --make-grm-bin --out sample --thread-num 10 &
But I ran into this error and it would be great if I can have some pointers about how I should proceed:
... Pruning SNPs with MAF > 0.01 ... After pruning SNPs with MAF > 0.01, there are 864803 SNPs (7439 SNPs with MAF < 0.01). terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc
Thank you!
KC
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Post by Jian Yang on Feb 26, 2014 4:19:29 GMT
It means that the machine runs out of memory. You can try the analysis in a machine with larger RAM.
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Post by chrchang on Feb 26, 2014 9:45:04 GMT
Shameless plug: PLINK 1.9 (https://www.cog-genomics.org/plink2/ ) has a memory-efficient --make-grm-bin implementation that will probably work here.
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