mpialign: 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 Debian possible default full paths are:

/usr/bin/mpialign - from package: zalign

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