bamToFastq: 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/bamToFastq - from package: BEDTools

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

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