fastq-dump: 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/fastq-dump - from package: sra-toolkit

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

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