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Just wondering if last printf END {printf ORS} might not be slightly improved as END {printf QRS} to suppress empty line for empty input.

Another working solution might be to change mkdir "$1" to env mkdir "$1"

It looks to me like your program can be fixed with just small changes to one line. I get the same output as R. Singh

change
NR == FNR {min[$1]=$2; max[$1]=$3; Gene[$6]=$NF; next}to
NR == FNR...