megablast: 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/megablast - from package: blast2
/usr/share/ncbi-blast+/bin/megablast - from package: ncbi-blast+-legacy

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

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