fastaq_to_fake_qual: 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/fastaq_to_fake_qual - from package: fastaq

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

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