fill-ref-md5: command not found

Have You tried accessing the binary with the full path?

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On CentOS possible default full paths are:

/usr/bin/fill-ref-md5 - from package: vcftools

You may install the required package with command yum install {package}

On Debian possible default full paths are:

/usr/bin/fill-ref-md5 - from package: vcftools

You may install the required package with command apt-get install {package}
Error in other languages:
fill-ref-md5: bevel nie gevind nie
fill-ref-md5: comandă negăsită
fill-ref-md5: comando não encontrado
fill-ref-md5: commande introuvable
fill-ref-md5: command not found
fill-ref-md5: käsku ei ole
fill-ref-md5: không tìm thấy lệnh
fill-ref-md5: komanda nerasta
fill-ref-md5: Kommando nicht gefunden.
fill-ref-md5: kommandot finns inte
fill-ref-md5: komut yok
fill-ref-md5: nie znaleziono polecenia
fill-ref-md5: níor aimsíodh an t-ordú
fill-ref-md5: no se encontró la orden
fill-ref-md5: no s'ha trobat l'ordre
fill-ref-md5: opdracht niet gevonden
fill-ref-md5: parancs nem található
fill-ref-md5: perintah tidak ditemukan
fill-ref-md5: príkaz nenájdený
fill-ref-md5: příkaz nenalezen
fill-ref-md5: команда не найдена
fill-ref-md5: командата не е открита
fill-ref-md5: 命令找不到
fill-ref-md5: コマンドが見つかりません