Post by Stark on Dec 23, 2015 12:23:36 GMT
Anybody can tell me what's wrong in my options? i want to performing the --mlma with a covar file, but my options doesn't produce a result?
This is my log file,is there a problem in Red Font part? how could i correct my options? Thanks
Options:
--mlma
--mlma-no-adj-covar
--bfile gcta_maf0.01
--grm maf0.01
--covar gcta_maf0.01.covar
--pheno maf0.01.phen
--out gcta_maf0.01
Note: This is a multi-thread program. You could specify the number of threads by the --thread-num option to speed up the computation if there are multiple processors in your machine.
Reading PLINK FAM file from [gcta_maf0.01.fam].
2592 individuals to be included from [gcta_maf0.01.fam].
Reading PLINK BIM file from [gcta_maf0.01.bim].
44046 SNPs to be included from [gcta_maf0.01.bim].
Reading PLINK BED file from [gcta_maf0.01.bed] in SNP-major format ...
Genotype data for 2592 individuals and 44046 SNPs to be included from [gcta_maf0.01.bed].
Reading phenotypes from [maf0.01.phen].
Non-missing phenotypes of 2592 individuals are included from [maf0.01.phen].
Reading discrete covariate(s) from [gcta_maf0.01.covar].
1 discrete covariate(s) of 2592 individuals are included from [gcta_maf0.01.covar].
Reading IDs of the GRM from [maf0.01.grm.id].
2592 IDs read from [maf0.01.grm.id].
Reading the GRM from [maf0.01.grm.bin].
Pairwise genetic relationships between 2592 individuals are included from [maf0.01.grm.bin].
2592 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).
2592 observations, 14 fixed effect(s), and 2 variance component(s)(including residual variance).
Calculating prior values of variance components by EM-REML ...
Analysis finished: Wed Dec 23 19:59:13 2015
Computational time: 0:0:3