Runtime differences between models

[John Meredith]

Hello,

I am working on running GWASs and have been struggling with runtime issues.

I am using a subset of 10,000 SNPs to benchmark how long it will take to run things.

I have two different models, one is a single factor model and another is a 3-factor model.

I'm running in parallel using 16GB Memory and 24 cores in a linux HPC environment, with the R multithreading variables maxed at 1 as per the documentation for linux systems.

The single factor runs the 10,000 SNPs in about 47 seconds, and the 3-factor model takes 25 minutes or more to complete, which would lead to very long compute times for a full GWAS with >7M SNPs. Is this difference in runtime expected for a more complicated model, or should I be concerned something else is wrong?

Best,
John

[Charleen Adams]

Thanks for asking this. I’m keenly interested in the answer, as well, as I have stopped a script with 6 factors that had been running for 4 days. Doing the math on what you provided, yours would seem to run for 12-13 days! I’ll also be watching with eager eyes. 🍿

Best,

Charleen

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[Aoife]

Thanks for asking this. I am also interested in this answer.

Best,

Aoife