How long does it takes to get Admixture analysis done?
Entering edit mode
3.6 years ago
lionair ▴ 10

Dear all,

I'd like to know how long does it usually takes for Admixture analysis to be done? I am using a 372G size VCF file which is a combination of SNPs from 1KGP, and another 3 populations. I tried the following commands and it took me ages to get it done. I'm just wondering if this is normal?

First run using 4 threads k=3 : 41days

./admixture_linux-1.3.0/admixture test1.bed 3 -j4 --cv=10

Second run using 50 threads k=4 : more than 30days (I killed the job)

nohup ./admixture_linux-1.3.0/admixture combined_pop.bed 4 -j50 --cv=10 2>21Sept17.err &

Third run using 128 threads k=4: It's been 6 days and still running.

nohup ./admixture_linux-1.3.0/admixture combined_pop.bed 4 -j128 --cv=10 2>21Sept17.err &

I'm just wondering if it is normal for Admixture to take long time to be done? If not, can all of you share the average duration for your analysis, parameter used and how many threads? My concern if the problem is actually from our server.

Thank you.

admixture SNP • 1.5k views

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