Post by adr on Jan 11, 2021 15:40:29 GMT
Dear all,
I tried to do a MLMA analysis with a covariate file, but without succes...
PS: without --mlma-no-preadj-covar option, everything is well.
Here the header of my file.phen:
Here the header of file.covar:
And my log file:
Anyone have any idea of the error?
Thanks !
I tried to do a MLMA analysis with a covariate file, but without succes...
PS: without --mlma-no-preadj-covar option, everything is well.
gcta64 --mlma --mlma-no-preadj-covar --bfile file --grm file --pheno file.phen --covar file.covar --out file --thread-num 14
sample1 sample1 0.64
sample2 sample2 1.38
sample3 sample3 -3.64
sample4 sample4 0.97
...
sample2 sample2 1.38
sample3 sample3 -3.64
sample4 sample4 0.97
...
Here the header of file.covar:
sample1 sample1 grp1
sample2 sample2 grp3
sample3 sample3 grp2
sample4 sample4 grp3
...
sample2 sample2 grp3
sample3 sample3 grp2
sample4 sample4 grp3
...
And my log file:
Accepted options:
--mlma
--mlma-no-preadj-covar
--bfile file
--grm file
--pheno file.phen
--covar file.covar
--out file
--thread-num 14
Note: the program will be running on 14 threads.
Reading PLINK FAM file from file.fam].
308 individuals to be included from [file.fam].
Reading PLINK BIM file from [file.bim].
1693910 SNPs to be included from [file.bim].
Reading PLINK BED file from [file.bed] in SNP-major format ...
Genotype data for 308 individuals and 1693910 SNPs to be included from [file.bed].
Reading phenotypes from [file.phen].
Non-missing phenotypes of 307 individuals are included from [file.phen].
Reading discrete covariate(s) from [file.covar].
1 discrete covariate(s) of 308 individuals are included from [file.covar].
Reading IDs of the GRM from [file.grm.id].
308 IDs read from [file.grm.id].
Reading the GRM from [file.grm.bin].
GRM for 308 individuals are included from [file.grm.bin].
307 individuals are in common in these files.
1 discrete variable(s) included as covariate(s).
Performing MLM association analyses (including the candidate SNP) ...
Performing REML analysis ... (Note: may take hours depending on sample size).
307 observations, 4 fixed effect(s), and 2 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Updated prior values: 44.0076 40.4843
logL: -815.675
Running AI-REML algorithm ...
Iter. logL V(G) V(e)
1 -800.09 47.01383 24.27078
2 -791.11 45.53321 20.95909
3 -789.27 44.31721 19.45211
4 -788.58 43.45948 18.63112
5 -788.29 41.58830 17.09379
6 -788.07 41.52499 17.31295
7 -788.06 41.56881 17.27816
8 -788.06 41.55912 17.28612
9 -788.06 41.56131 17.28433
Log-likelihood ratio converged.
Calculating allele frequencies ...
Running association tests for 1693910 SNPs ...
Error: Xt_Vi_X is not invertable.
An error occurs, please check the options or data
--mlma
--mlma-no-preadj-covar
--bfile file
--grm file
--pheno file.phen
--covar file.covar
--out file
--thread-num 14
Note: the program will be running on 14 threads.
Reading PLINK FAM file from file.fam].
308 individuals to be included from [file.fam].
Reading PLINK BIM file from [file.bim].
1693910 SNPs to be included from [file.bim].
Reading PLINK BED file from [file.bed] in SNP-major format ...
Genotype data for 308 individuals and 1693910 SNPs to be included from [file.bed].
Reading phenotypes from [file.phen].
Non-missing phenotypes of 307 individuals are included from [file.phen].
Reading discrete covariate(s) from [file.covar].
1 discrete covariate(s) of 308 individuals are included from [file.covar].
Reading IDs of the GRM from [file.grm.id].
308 IDs read from [file.grm.id].
Reading the GRM from [file.grm.bin].
GRM for 308 individuals are included from [file.grm.bin].
307 individuals are in common in these files.
1 discrete variable(s) included as covariate(s).
Performing MLM association analyses (including the candidate SNP) ...
Performing REML analysis ... (Note: may take hours depending on sample size).
307 observations, 4 fixed effect(s), and 2 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Updated prior values: 44.0076 40.4843
logL: -815.675
Running AI-REML algorithm ...
Iter. logL V(G) V(e)
1 -800.09 47.01383 24.27078
2 -791.11 45.53321 20.95909
3 -789.27 44.31721 19.45211
4 -788.58 43.45948 18.63112
5 -788.29 41.58830 17.09379
6 -788.07 41.52499 17.31295
7 -788.06 41.56881 17.27816
8 -788.06 41.55912 17.28612
9 -788.06 41.56131 17.28433
Log-likelihood ratio converged.
Calculating allele frequencies ...
Running association tests for 1693910 SNPs ...
Error: Xt_Vi_X is not invertable.
An error occurs, please check the options or data
Anyone have any idea of the error?
Thanks !