Extremely slow when conducting genome-wide multi-trait analysis

[ryshi06]

Hi,

I have a small cohort of about 90 individuals, and 4 phenotypes of interests. I was using the command

gemma -bfile ./output/ABCDS_multitrait_AmyloidPET_Tau_residuals -maf 0.01 -d ./output/ABCDS_GEMMA_AmyloidPET_Tau.eigenD.txt -u ./output/ABCDS_GEMMA_AmyloidPET_Tau.eigenU.txt -lmm 4 -n 1 2 3 4 5 -o ABCDS_AmyloidPET_Tau_MAF01

to run genome-wide multi-trait analyses.

However, after 6 hours, it only read in 1% of SNPs, so I don't quite understand what is happening here. To run this job, we set 1 CPU and 256GB memories. I am wondering if is this normal or not. Also, can I have a solution for this?

Thank you!

Best,
Ruyu