nuitka-run: 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/nuitka-run - from package: nuitka
/usr/share/nuitka/bin/nuitka-run - from package: nuitka

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