Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Gemma run-time for Estimate Relatedness Matrix calculation #265

Open
alviitayyaba opened this issue Jun 6, 2022 · 0 comments
Open

Gemma run-time for Estimate Relatedness Matrix calculation #265

alviitayyaba opened this issue Jun 6, 2022 · 0 comments

Comments

@alviitayyaba
Copy link

alviitayyaba commented Jun 6, 2022

Hi,
I am new to GWAS. I have dataset of 15K+ individuals and 200+ SNPs. I wanted to estimate the relatedness matrix, I used the following command.

gemma -bfile data_QC -gk 1 -o data_QC_gem

GEMMA 0.98.3 (2020-11-28) by Xiang Zhou and team (C) 2012-2020
Reading Files ...

number of total individuals = 15628

number of analyzed individuals = 2904

number of covariates = 1

number of phenotypes = 1

number of total SNPs/var = 270047

number of analyzed SNPs = 260663

Calculating Relatedness Matrix ...
======= 15%

It's been running for 4+ hours.
How much time it will take to complete?
Does it depend on computational resources on my machine?
Any help in this regard would be appreciated.
Thank you

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant