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Jiaxin-Fan / ASEP

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high memory requested #9

Open ggabelli opened 3 years ago

ggabelli commented 3 years ago

Hi I wish to use ASEP to analyze a dataset of 90 samples. Every sample has 10/20 snps (on an average gene). I have a limit of 60gb of memory and in nearly all cases it's not enough to complete the analysis. I tried to lower the number of permutation down to 10e3, but it didn't help much. Is that normal? I am doing some mistakes? Thanks

Jiaxin-Fan commented 3 years ago

typically 10e3 should work. the memory would be huge if permutation goes to/over 10e5. I would suggest run one gene to check if the code is correct. in addition, if you have limited memory, I would suggest run one gene at a time, write the output to file, clear the memory/cache, and then go on to the next gene. Hope that help!