alleles=$1
classes=$2
snploc=$3
out=$4

dir=`pwd`

# set the appropriate directory for rfmix program
cd /usr/local/RFMix-1.5.4/

python2.7 RunRFMix.py PopPhased ${dir}/$alleles ${dir}/$classes ${dir}/$snploc -o ${dir}/$out --disable-parallel -n 5

cd $dir