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statgen / Minimac4

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minimac4 core dumped issue with 57K and above sample size #9

Open wmulla opened 6 years ago

wmulla commented 6 years ago

Hello, I've been trying to run Minimac4 to impute a cohort of roughly 225,000 individuals. When attempted to impute a total of 1142 chunks of 5 Mb +/- 1 Mb, 5 chunks were failed due to core dump error, remaining 1137 chunks imputed successfully. So I split each of 5 chunks equally into two, resulting into 10 chunks with a sample size ~ 110 K individuals and reran the imputation. From this attempt, only two out of 10 chunks were rescued but they were not belonging to the same original chunk with 225K individuals. Remaining 8 chunks with 110K sample size failed due to core dump issue. So again, chunks with 110K samlpe size were split into 55K sample size and reran imputation, this time no chunks passed, all of them failed due to same core dump issue. Are you aware of any bugs in the software that would produce this error type? Thank you.

Santy-8128 commented 6 years ago

I am guessing this might have to do with memory error ? Maybe try running them with --cpu 1 (by default it runs on 5 CPUs so your memory might be overflowing.

Regards, Sayantan Das,

23andMe

On Wed, Sep 5, 2018 at 12:48 PM wmulla notifications@github.com wrote:

Hello, I've been trying to run Minimac4 to impute a cohort of roughly 225,000 individuals. When attempted to impute a total of 1142 chunks of 5 Mb +/- 1 Mb, 5 chunks were failed due to core dump error, remaining 1137 chunks imputed successfully. So I split each of 5 chunks equally into two, resulting into 10 chunks with a sample size ~ 110 K individuals and reran the imputation. From this attempt, only two out of 10 chunks were rescued but they were not belonging to the same original chunk with 225K individuals. Remaining 8 chunks with 110K sample size failed due to core dump issue. So again, chunks with 110K samlpe size were split into 55K sample size and reran imputation, this time no chunks passed, all of them failed due to same core dump issue. Are you aware of any bugs in the software that would produce this error type? Thank you.

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