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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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REGENIE imputed array association analysis unexpected lines #126

Open Shicheng-Guo opened 3 years ago

Shicheng-Guo commented 3 years ago

Here is an interesting unexpected thing. You can find REGENIE generated extra 4 lines for chr4 (UKB imputed array), rs530960215 is the last SNPs, but I don't know why REGENIE have extra 4 line result (9 columns)

4 191035507 rs550165809 A C 0.000581789 416818 ADD -0.253168 0.200554 1.59352 0.684398
4 191037826 rs561400877 C G 3.58835e-05 418019 ADD 0.0392336 0.756786 0.00268763 0.018338
4 191041615 rs558880772 A G 6.45582e-05 418227 ADD 0.201398 0.578166 0.12134 0.138116
4 191041711 rs572040912 G T 0.000843376 417963 ADD 0.0442757 0.167076 0.0702268 0.10182
4 191043204 rs530960215 C T 5.50158e-05 418062 ADD -0.296431 0.635266 0.217739 0.193299
0 0    0.0001752 416667 ADD 0.111018 0.364736 0.092646 0.118707
0 0    0.0001752 416667 ADD 0.111018 0.364736 0.092646 0.118707
0 0    0.0001752 416667 ADD 0.111018 0.364736 0.092646 0.118707
0 0    0.0001752 416667 ADD 0.111018 0.364736 0.092646 0.118707

(base) [sguo2@login01 gwas]$ regenie |============================| | REGENIE v2.0.2 | |============================|

Copyright (c) 2020 Joelle Mbatchou and Jonathan Marchini. Distributed under the MIT License.

ERROR: You must provide an output prefix using '--out' For more information, use option '--help' or visit the website: https://rgcgithub.github.io/regenie/

joellembatchou commented 3 years ago

We'll take a closer look to identify the cause of this.

Cheers, Joelle

Shicheng-Guo commented 3 years ago

File size should be one of the reasons since I tried to use head -n 20000 *bim to repeat the same command and the result are quite good. However, when I used full plink genotype data, the last several blocks will show an error.