Error when making a GRM from bgen files

khm
New Member

Posts: 1

Error when making a GRM from bgen files Apr 2, 2020 2:22:50 GMT

Quote

Post by khm on Apr 2, 2020 2:22:50 GMT

Hi all,

I am trying to make a GRM from bgen files. I followed all the instructions (such as making bgi files, storing the genotype posterior probabilities in 8 bits, compressing the data in zstd format) for using bgen files as inputs.

The GCTA website says that multiallelic SNPs will be ignored automatically, but I keep getting an error saying that there are multiallelic SNPs. Also, problematic SNPs identified in this error message keep changing every time I run it. Yet, when I examine the data manually, I really do not find multiallelic SNPs.

Also, when I run this on our linux server, I keep getting "Illegal instruction (core dump)" error, which I don't on my local laptop.

Am I doing something wrong or is it an error in gcta software?

Thanks!

dvh13 New Member Posts: 5	Error when making a GRM from bgen files Apr 9, 2020 15:41:14 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by dvh13 on Apr 9, 2020 15:41:14 GMT the answer to the 'illegal instruction' is you need an avx2 chip (on our cluster have to specify that directly) bw (now I will ask my seg fault question!)

gpcr
New Member

Posts: 5

Error when making a GRM from bgen files Apr 24, 2020 20:45:19 GMT

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Post by gpcr on Apr 24, 2020 20:45:19 GMT

Iam getting below error when trying to generate the GRM using list of bgen files
Am I missing any files? do we need to provide "sample" file?

$gcta64 --mbgen bgen.list.tsv --make-grm --thread-num 28 --out OUTPUT
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.93.1f beta Linux
* (C) 2010-present, The University of Queensland
* Please report bugs to Jian Yang <jian.yang@uq.edu.au>
*******************************************************************
Analysis started at 16:34:43 EDT on Fri Apr 24 2020.
Hostname: x12345

Options:

--mbgen bgen.list.tsv
--make-grm
--thread-num 28
--out OUTPUT

The program will be running on up to 28 threads.
Note: GRM is computed using the SNPs on the autosome.
Error: no phenotype file presents
An error occurs, please check the options or data

gpcr New Member Posts: 5	Error when making a GRM from bgen files Apr 24, 2020 20:54:42 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by gpcr on Apr 24, 2020 20:54:42 GMT After adding a sample file to the input through --sample, getting an error with a core dump "Segmentation fault (core dumped)"

Post by khm on Apr 2, 2020 2:22:50 GMT

Post by dvh13 on Apr 9, 2020 15:41:14 GMT

Post by gpcr on Apr 24, 2020 20:45:19 GMT

Post by gpcr on Apr 24, 2020 20:54:42 GMT