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bmvdgeijn / WASP

WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
Apache License 2.0
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speedup for fit_as_coefficients? #97

Closed lw157 closed 4 years ago

lw157 commented 4 years ago

Hi Graham/Bryce, The fit_as_coefficients has been running for 5 days. From the "std" print out, it was about 3 days to process one sample, but I have about 50 samples, so it will take 150 days?

Can I run each sample separately? Or should I skip some loci, such as skip option for fit_bnb_coefficients?

Do you have any other suggestion that could speedup this step? Thanks a lot. Best, Liuyang

bmvdgeijn commented 4 years ago

Hi Liuyang,

I believe this is another case where skipping many of the loci will be your best bet. You don’t need 2 million loci to estimate one parameter.

Bryce

Sent from my iPhone

On Jun 8, 2020, at 9:54 AM, Liuyang Wang notifications@github.com wrote:

 Hi Graham, The fit_as_coefficients has been running for 5 days. From the "std" print out, it was about 3 days to process one sample, but I have about 50 samples, so it will take 150 days? Can I run each sample separately? Or should I skip some loci, such as skip option for fit_bnb_coefficients? Do you have any other suggestion that could speedup this step? Thanks a lot. Best, Liuyang

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lw157 commented 4 years ago

Hi Liuyang, I believe this is another case where skipping many of the loci will be your best bet. You don’t need 2 million loci to estimate one parameter. Bryce … Sent from my iPhone On Jun 8, 2020, at 9:54 AM, Liuyang Wang @.***> wrote:  Hi Graham, The fit_as_coefficients has been running for 5 days. From the "std" print out, it was about 3 days to process one sample, but I have about 50 samples, so it will take 150 days? Can I run each sample separately? Or should I skip some loci, such as skip option for fit_bnb_coefficients? Do you have any other suggestion that could speedup this step? Thanks a lot. Best, Liuyang — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

Hi Bryce, I will add the skip option to this function. Thanks for your suggestions. Cool. Best, Liuyang