subtractBed: 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 CentOS possible default full paths are:

/usr/bin/subtractBed - from package: BEDTools

You may install the required package with command yum install {package}

On Debian possible default full paths are:

/usr/bin/subtractBed - from package: BEDTools

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

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