nenctool: command not found

Have You tried accessing the binary with the full path?

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/nenctool - from package: sra-toolkit

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