yubikey-totp: 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/yubikey-totp - from package: python-yubico-tools

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