Estimate cost of GWAS regression steps

[eric-czech]

This is an estimate of the VM rental time necessary to do the GWAS regressions (similar to https://github.com/related-sciences/ukb-gwas-pipeline-nealelab/issues/8).

Here are current figures:

• There are 1760 phenotypes that need to be processed
  • The Neale Lab results contain 2891 phenotypes and the OT sumstats contain files for this many phenotypes as well
  • Our run of PHESANT, on a slightly different set of samples, produced 5384 phenotypes
  • There are 1760 in the intersection of the two
• Running phenotypes on chr21 (141,910 variants) for 11 hr 5 mins produced results for 265 phenotypes when using a cluster of 60 n1-highmem-16 instances
• The processing rate is then 141,910 variants * 265 phenotypes / 665 minutes = 942.51 phenotype-variant / second
  • For chr21, this equates to (665*60) / 265 = ~150 seconds per phenotype
• For 10,691,206 variants over all contigs and 1,760 phenotypes, this implies a total processing time of ((10,691,206*1,760) / 942.51) / 86400 = ~231 days

A ballpark cost to keep a cluster of this size running that long is 60 nodes (231 days 24 hrs) * $0.946424/hr = $314,818.

Clearly we have got to find some room to improve this.

[eric-czech]

On instance pricing:

• Switching to standard instead of highmem instances would bring costs down by a factor of .8 (so 80% of original)
• Moving to preemptible instances would bring costs down by a factor of .21

If various dask memory issues could be solved and we could use preemptible standard instances, the total cost would be around $53k.

[ravwojdyla]

@eric-czech I assume this stat:

Running phenotypes on chr21 (141,910 variants) for 11 hr 5 mins produced results for 265 phenotypes when using a cluster of 60 n1-highmem-16 instances

and this comment https://github.com/pystatgen/sgkit/issues/390#issuecomment-748205731 are for the same run, correct? And if it is, how is the 11 hr 5 mins here, connected with about 2hrs it took to run the regressions for chr21?

[eric-czech]

and this comment pystatgen/sgkit#390 (comment) are for the same run, correct?

No, that caption is definitely misleading -- I was either wrong when I wrote it or trying to make it clear that the individual phenotypes can be seen as single spikes. Here is a full version of that readout that also includes the run of the 265 phenotypes: