Hello, I'm using your tool gcta-fastgwasGLMM, it's a great tool helped me a lot.
But I am having a problem that my sample size is now 300,000 and SNP count is one million, but it keeps on getting stuck in the grid search above for a month without being able to produce any results, why is that?
Can you guys see what's wrong with my command?
The program will be running with up to 24 threads.
Reading PLINK FAM file from [/ukb/qqpcmr_system/gwas/chr2_QC.fam]...
337056 individuals to be included from FAM file.
Reading phenotype data from [/ukb/qqpcmr_system/gwas/ca.txt]...
337056 overlapping individuals with non-missing data to be included from the phenotype file.
337056 individuals to be included. 156073 males, 180983 females, 0 unknown.
Reading PLINK BIM file from [/ukb/qqpcmr_system/gwas/chr2_QC.bim]...
1037533 SNPs to be included from BIM file(s).
Reading the sparse GRM file from [/ukb/qqpcmr_system/gwas/chr2_sp_grm]...
After matching all the files, 337056 individuals to be included in the analysis.
Estimating the genetic variance (Vg) by fastGWA-REML (grid search)...
Hello, I'm using your tool gcta-fastgwasGLMM, it's a great tool helped me a lot. But I am having a problem that my sample size is now 300,000 and SNP count is one million, but it keeps on getting stuck in the grid search above for a month without being able to produce any results, why is that? Can you guys see what's wrong with my command?
Analysis started at 12:46:25 CST on Sat Dec 23 2023. Hostname: labxserver2-R5215-A12
Options:
--bfile /ukb/qqpcmr_system/gwas/chr2_QC --grm-sparse /ukb/qqpcmr_system/gwas/chr2_sp_grm --fastGWA-mlm --pheno /ukb/qqpcmr_system/gwas/ca.txt --thread-num 24 --out /ukb/qqpcmr_system/gwas_output/geno_ca_chr2
The program will be running with up to 24 threads. Reading PLINK FAM file from [/ukb/qqpcmr_system/gwas/chr2_QC.fam]... 337056 individuals to be included from FAM file. Reading phenotype data from [/ukb/qqpcmr_system/gwas/ca.txt]... 337056 overlapping individuals with non-missing data to be included from the phenotype file. 337056 individuals to be included. 156073 males, 180983 females, 0 unknown. Reading PLINK BIM file from [/ukb/qqpcmr_system/gwas/chr2_QC.bim]... 1037533 SNPs to be included from BIM file(s). Reading the sparse GRM file from [/ukb/qqpcmr_system/gwas/chr2_sp_grm]... After matching all the files, 337056 individuals to be included in the analysis. Estimating the genetic variance (Vg) by fastGWA-REML (grid search)...