How to simulate 100k samples having 40 million SNPs in a proportion of case:control=30:70?
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4.3 years ago
b.ambrozio ▴ 30

Hi there,

I need to perform a stress test in a GWAS tool and the duty demands a dataset (plink format) having 100 thousand samples, having 40 million SNPs in a proportion of case:control=30:70.

I'm performing the command:

plink1.9 --simulate ds1.sim --make-bed --out ds1 --simulate-ncases 30000 --simulate-ncontrols 70000

But after about 3 hours execution, I'm facing Error: File write failure., even though my environment has 256T of disk. (It's a container with a S3 (Object store) mounted through s3fs).

I was wondering if there's a clever way to do that? Perhaps breaking it into small chunks and merging up later somehow? It would prevent me to be waiting hours till a error happens and I loose either time and the sample generated so far.

Thanks in advance!

plink gwas • 793 views
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s3fs has a maximum file size (which depends on the multipart_size parameter). Check that you're not exceeding this.

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Hello b.ambrozio!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/11373

This is typically not recommended as it runs the risk of annoying people in both communities.

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Sorry about that. I'm new on bioinformatics, not sure which community should I use...

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