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rgcgithub / regenie

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
https://rgcgithub.github.io/regenie
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step 1 error #97

Closed paniscusJr closed 3 years ago

paniscusJr commented 3 years ago

I’m getting the following error when I run step 1 using the UK Biobank data. I am running regenie from the docker image (v2.0.1). I made sure that I have permissions to write in the tmpdir directory. The output seems ok and was able to complete step 2.

From step 1 log:

Level 1 ridge... -on phenotype 1 (ldl_direct_f30780_0_0)...ERROR : Cannot read temporary /tmpdir/regenie_tmp_preds_l0_Y1 min value 0.75 : Rsq = 0.0975257, MSE = 0.902398 0.99 : Rsq = 0.0975526, MSE = 0.902522

List of blup files written to: [/02_GWAS/ukb_step1_LDL_pred.list]

joellembatchou commented 3 years ago

Hi,

Is the output you posted exactly what is printed in the log? (The format of the ERROR message does not match with what is coded in C++). Furthermore, the software should exit after the error message so it is strange it keeps on running.

Could you retry with the newest docker image (for Regenie v2.0.2)?

Cheers, Joelle