intersectBed: 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/intersectBed - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/intersectBed - from package: BEDTools

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

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