pythontex3: 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/pythontex3 - from package: texlive-extra-utils

You may install the required package with command apt-get install {package}
Error in other languages:
pythontex3: bevel nie gevind nie
pythontex3: comandă negăsită
pythontex3: comando não encontrado
pythontex3: commande introuvable
pythontex3: command not found
pythontex3: käsku ei ole
pythontex3: không tìm thấy lệnh
pythontex3: komanda nerasta
pythontex3: Kommando nicht gefunden.
pythontex3: kommandot finns inte
pythontex3: komut yok
pythontex3: nie znaleziono polecenia
pythontex3: níor aimsíodh an t-ordú
pythontex3: no se encontró la orden
pythontex3: no s'ha trobat l'ordre
pythontex3: opdracht niet gevonden
pythontex3: parancs nem található
pythontex3: perintah tidak ditemukan
pythontex3: príkaz nenájdený
pythontex3: příkaz nenalezen
pythontex3: команда не найдена
pythontex3: командата не е открита
pythontex3: 命令找不到
pythontex3: コマンドが見つかりません