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omerwe / polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)
MIT License
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Memory Issues with polyfun.py #162

Closed BideZ closed 1 year ago

BideZ commented 1 year ago

Hi Omer,

I am now trying to calculate prior using polyfun.py. I am using the baseline annotations provided in the Wiki page, but it ended up taking me around ~90G RAM and ultimately ran into a memory error. I would like to ask if there is a possibility where I could configure the memory taken up by polyfun or do I have to filter the baseline annotations so my memory will not explode when loading them?

I am looking forward to your response!

Thanks !

Best, Bide

omerwe commented 1 year ago

Hi @BideZ, PolyFun does take lots of memory, human genomes are big 🤷 If you can't get more memory, then you'd have to filter out either your annotations or your SNPs (none is ideal). Hope this helps somewhat, sorry I can't help more!

BideZ commented 1 year ago

Thanks for your comment Omer!

I solved the problem with running it in another server which has more memory :)

Cheers

Best, Bide