yubikeyd: 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/sbin/yubikeyd - from package: yubikey-server-c

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