relion_run_ctffind: 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/relion_run_ctffind - from package: relion-bin+gui
/usr/bin/relion_run_ctffind - from package: relion-bin+mpi+gui
/usr/bin/relion_run_ctffind - from package: relion-bin+mpi
/usr/bin/relion_run_ctffind - from package: relion-bin

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

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