Will Plink and GCTA match and reorder sample order?

Question

[Mian]

Will Plink and GCTA will match and reorder the sample order from covariates or phenotypes files to genotypes file sample order?

1. plink --bfile ${AD_geno}_1 --covar Covariates_AVD.txt --write-covar --dummy-coding
2. ${GCTA} --grm kinship_AVD --bfile ${AD_geno}_1 --pheno Pheno_AVD.txt

Today, I realized that the sample order in Covariates_AVD.txt and Pheno_AVD.txt are different with ${AD_geno}_1.fam. Does it matter? I have finished this project several month ago. Afraid to come back.