makeblastdb: 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/makeblastdb - from package: ncbi-blast+

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

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