[Bug]: ./10a-gwas_aar.sh: Error: the V matrix is not invertible

[ks164]

Contact Details

ks164@duke.edu

Scripts

10a-gwas_aar.sh

What happened?

Running fastGWA on twin (MZ and DZ) data gives the following error:

Estimating the genetic variance (Vg) by fastGWA-REML (grid search)... Error: the V matrix is not invertible.

the input files data_fast.grm.sp contains 2175 pairs and data_fast.grm.id contains 1502 individuals in case it helps.

full log output below.

How can the bug be reproduced?

No response

R version

4.3.3 (February, 2024)

Python version

None

Relevant log output

*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version v1.94.1 Linux
* Built at Nov 15 2022 21:14:25, by GCC 8.5
* (C) 2010-present, Yang Lab, Westlake University
* Please report bugs to Jian Yang <jian.yang@westlake.edu.cn>
*******************************************************************
Analysis started at 12:22:33 EDT on Mon Oct 21 2024.
Hostname: dcc-login-01

Options: 

--grm /hpc/group/sugdenlab/godmc_phase2/ERisk/processed_data/genetic_data/data 
--make-bK-sparse 0.05 
--autosome 
--out /hpc/group/sugdenlab/godmc_phase2/ERisk/processed_data/genetic_data/data_fast 
--thread-num 16 

The program will be running with up to 16 threads.
Pruning the GRM to a sparse matrix with a cutoff of 0.050000...
Total number of parts to be processed: 1
    Saving 1502 individual IDs
    Processing part 1
Saving the sparse GRM (2175 pairs) to [/hpc/group/sugdenlab/godmc_phase2/ERisk/processed_data/genetic_data/data_fast.grm.sp]
finished generating a sparse GRM Success:

Analysis finished at 12:22:33 EDT on Mon Oct 21 2024
Overall computational time: 0.58 sec.
Done on making bK sparse
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version v1.94.1 Linux
* Built at Nov 15 2022 21:14:25, by GCC 8.5
* (C) 2010-present, Yang Lab, Westlake University
* Please report bugs to Jian Yang <jian.yang@westlake.edu.cn>
*******************************************************************
Analysis started at 12:22:33 EDT on Mon Oct 21 2024.
Hostname: dcc-login-01

Options: 

--bfile /hpc/group/sugdenlab/godmc_phase2/ERisk/processed_data/genetic_data/data 
--grm-sparse /hpc/group/sugdenlab/godmc_phase2/ERisk/processed_data/genetic_data/data_fast 
--fastGWA-mlm 
--mpheno 1 
--pheno age_acc.plink 
--h2-limit 20 
--out /hpc/group/sugdenlab/godmc_phase2/ERisk/results/10/DNAmAgeSD 

Reading PLINK FAM file from [/hpc/group/sugdenlab/godmc_phase2/ERisk/processed_data/genetic_data/data.fam]...
1502 individuals to be included from FAM file.
Reading phenotype data from [age_acc.plink]...
1502 overlapping individuals with non-missing data to be included from the phenotype file.
1502 individuals to be included. 762 males, 740 females, 0 unknown.
Reading PLINK BIM file from [/hpc/group/sugdenlab/godmc_phase2/ERisk/processed_data/genetic_data/data.bim]...
7159238 SNPs to be included from BIM file(s).
Reading the sparse GRM file from [/hpc/group/sugdenlab/godmc_phase2/ERisk/processed_data/genetic_data/data_fast]...
After matching all the files, 1502 individuals to be included in the analysis.
Estimating the genetic variance (Vg) by fastGWA-REML (grid search)...
Error: the V matrix is not invertible.
An error occurs, please check the options or data

[SiyiSEA]

Hi,

Sorry for late respond.

May I know who many rows in both /hpc/group/sugdenlab/godmc_phase2/ERisk/processed_data/genetic_data/data_fast.grm.sp and /hpc/group/sugdenlab/godmc_phase2/ERisk/processed_data/genetic_data/data_fast.grm.id ?

[ks164]

Hi Siyi,

data_fast.grm.sp contains 2175 pairs and data_fast.grm.id contains 1502 individuals

[ZXiaopu]

Hi Siyi,

I got the same issue when running MZ twins (689 individuals in total).

my data_fast.grm.sp contains 897 rows and data_fast.grm.id contains 689 rows