nucmer: command not found

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/nucmer - from package: mummer

You may install the required package with command apt-get install {package}

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