Post by moldach on Jan 25, 2019 17:56:31 GMT
I keep getting a message saying "killed" when trying to do the segment based LD score step on my data which makes me think it's a memory issue.
In the basic GREML tutorial it suggests you can split up the data by chromosome, like so:
So that I would have stratified SNPs by segment-based LD score for each chromosome and then make GRMs for each of these groups:
gcta64 --bfile test --ld-score-region 200 --out testIn the basic GREML tutorial it suggests you can split up the data by chromosome, like so:
gcta64 --bfile test --chr 1 --maf 0.01 --make-grm --out test_chr1 --thread-num 10
gcta64 --bfile test --chr 2 --maf 0.01 --make-grm --out test_chr2 --thread-num 10
...
gcta64 --bfile test --chr 22 --maf 0.01 --make-grm --out test_chr22 --thread-num 10Is it possible to do something similar for GREML in WGS or imputed data? For example:
gcta64 --bfile test --chr 1 --ld-score-region 200 --out test_chr1
gcta64 --bfile test --chr 2 --ld-score-region 200 --out test_chr2
...
lds_seg = read.table("test_ch1.score.ld",header=T,colClasses=c("character",rep("numeric",8)))
lds_seg = read.table("test_ch2.score.ld",header=T,colClasses=c("character",rep("numeric",8)))
...So that I would have stratified SNPs by segment-based LD score for each chromosome and then make GRMs for each of these groups:
chr1_snp_group1.txt
chr1_snp_group2.txt
chr1_snp_group3.txt
chr1_snp_group4.txt
...
chr22_snp_group1.txt
chr22_snp_group2.txt
chr22_snp_group3.txtAnd then perform the REML analysis on those 88 GRMs? Just wondering if that's a valid approach or if there's some way to deal with out-of-memory issues with large GWAS/imputed data?
Another question is how do you submit gcta64 properly on PBS with qsub to parallelize?
In the PBS script I specify "#PBS -l nodes=1:ppn=10" and for the gcta command I'm putting --thread-num 10; however, according to htop it looks like it's only using one thread?
Another question is how do you submit gcta64 properly on PBS with qsub to parallelize?
In the PBS script I specify "#PBS -l nodes=1:ppn=10" and for the gcta command I'm putting --thread-num 10; however, according to htop it looks like it's only using one thread?
