md5fa: 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

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/md5fa - from package: samtools

You may install the required package with command yum install {package}
Error in other languages:
md5fa: bevel nie gevind nie
md5fa: comandă negăsită
md5fa: comando não encontrado
md5fa: commande introuvable
md5fa: command not found
md5fa: käsku ei ole
md5fa: không tìm thấy lệnh
md5fa: komanda nerasta
md5fa: Kommando nicht gefunden.
md5fa: kommandot finns inte
md5fa: komut yok
md5fa: nie znaleziono polecenia
md5fa: níor aimsíodh an t-ordú
md5fa: no se encontró la orden
md5fa: no s'ha trobat l'ordre
md5fa: opdracht niet gevonden
md5fa: parancs nem található
md5fa: perintah tidak ditemukan
md5fa: príkaz nenájdený
md5fa: příkaz nenalezen
md5fa: команда не найдена
md5fa: командата не е открита
md5fa: 命令找不到
md5fa: コマンドが見つかりません