MLMA and chromosome X

Hi everyone

My apologies if this is a question that has already been answered or documented, I did look but didn't find anything so hopefully you can help me!

I am just trying to run mlma-loco but chromosome x seems to be ignored. Is there a flag that I should be including? Here is the code:

gcta \
 --bfile ${bfile} \
 --mlma-loco \
 --pheno ${phen} \
 --qcovar ${covariates} \
 --out ${out} \
 --thread-num ${nthreads}

Thanks!

Gib