RNAeffective: 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/RNAeffective - from package: rnahybrid

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

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