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Post by auzzie599 on Nov 12, 2021 18:22:41 GMT
Hello, I'm trying to construct a GRM using a large dataset (>10k individuals, >140million sites). I am splitting up the process into 200 parts using the --make-grm-part option.
My code is:
for i in {1..200}; do gcta64 --bfile INPUT --make-grm-part 200 $i --thread-num 10 --out testOUT; done
Parts 1 through 196 seem to finish just fine. But parts 197 through 200 result in segfaults. It looks like, starting with part 197, the program is trying to construct a GRM for people that do not exist in the dataset (see output below). You can see that the program is trying to compute the GRM for individuals 10406-10432, although there are only 10418 individuals total in the dataset. The same issue occurs for parts 198,199, and 200. Any ideas what is going on here?
Options:
--bfile INPUT --make-grm-part 200 197 --thread-num 10 --out testOUT
The program will be running on up to 10 threads. Note: GRM is computed using the SNPs on the autosome. Reading PLINK FAM file from [/path/to/INPUT]... 10418 individuals to be included from FAM file. 10418 individuals to be included. 0 males, 0 females, 10418 unknown. Reading PLINK BIM file from [path/to/INPUT]... 146103976 SNPs to be included from BIM file(s). Computing the genetic relationship matrix (GRM) v2 ... Subset 197/200, no. subject 10406-10432 27 samples, 146103976 markers, 281313 GRM elements
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