Post by jramirezdiaz on Aug 5, 2022 17:01:56 GMT
I received an error when I am running GCTA analysis with fastGWA-mlm-binary, Error: XtWX is not invertible.
I try running the analysis without covariates or with a reduction to 3 cov, but the result is the same
any help?
Thanks in advance
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version v1.94.1 Linux
* (C) 2010-present, Yang Lab, Westlake University
* Please report bugs to Jian Yang <jian.yang@westlake.edu.cn>
*******************************************************************
Analysis started at 18:52:36 CEST on Fri Aug 05 2022.
Hostname: pam-HP-Z4-G4-Workstation
Options:
--bfile geno_vdb
--grm-sparse GCTAsparsegrm
--fastGWA-mlm-binary
--pheno vdb_phe_gcta.txt
--qcovar vdb_cov_gcta.txt
--covar vdb_fe_gcta.txt
--thread-num 10
--out sparse_assoc_glmm
The program will be running with up to 10 threads.
Reading PLINK FAM file from [geno_vdb.fam]...
247 individuals to be included from FAM file.
Reading phenotype data from [vdb_phe_gcta.txt]...
247 overlapping individuals with non-missing data to be included from the phenotype file.
247 individuals to be included. 0 males, 0 females, 247 unknown.
Reading PLINK BIM file from [geno_vdb.bim]...
32062 SNPs to be included from BIM file(s).
Reading quantitative covariates from [vdb_cov_gcta.txt].
10 covariates of 247 samples to be included.
Reading discrete covariates from [vdb_fe_gcta.txt].
1 covariates of 247 samples to be included.
10 qcovar, 1 covar and 0 rcovar to be included.
247 common individuals among the covariate files to be included.
247 overlapping individuals with non-missing data to be included from the covariate file(s).
Reading the sparse GRM file from [GCTAsparsegrm]...
After matching all the files, 247 individuals to be included in the analysis.
Performing GLM to get the starting values of beta for the covariates...
Error: XtWX is not invertible.
An error occurs, please check the options or data
I try running the analysis without covariates or with a reduction to 3 cov, but the result is the same
any help?
Thanks in advance
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version v1.94.1 Linux
* (C) 2010-present, Yang Lab, Westlake University
* Please report bugs to Jian Yang <jian.yang@westlake.edu.cn>
*******************************************************************
Analysis started at 18:52:36 CEST on Fri Aug 05 2022.
Hostname: pam-HP-Z4-G4-Workstation
Options:
--bfile geno_vdb
--grm-sparse GCTAsparsegrm
--fastGWA-mlm-binary
--pheno vdb_phe_gcta.txt
--qcovar vdb_cov_gcta.txt
--covar vdb_fe_gcta.txt
--thread-num 10
--out sparse_assoc_glmm
The program will be running with up to 10 threads.
Reading PLINK FAM file from [geno_vdb.fam]...
247 individuals to be included from FAM file.
Reading phenotype data from [vdb_phe_gcta.txt]...
247 overlapping individuals with non-missing data to be included from the phenotype file.
247 individuals to be included. 0 males, 0 females, 247 unknown.
Reading PLINK BIM file from [geno_vdb.bim]...
32062 SNPs to be included from BIM file(s).
Reading quantitative covariates from [vdb_cov_gcta.txt].
10 covariates of 247 samples to be included.
Reading discrete covariates from [vdb_fe_gcta.txt].
1 covariates of 247 samples to be included.
10 qcovar, 1 covar and 0 rcovar to be included.
247 common individuals among the covariate files to be included.
247 overlapping individuals with non-missing data to be included from the covariate file(s).
Reading the sparse GRM file from [GCTAsparsegrm]...
After matching all the files, 247 individuals to be included in the analysis.
Performing GLM to get the starting values of beta for the covariates...
Error: XtWX is not invertible.
An error occurs, please check the options or data