multiIntersectBed: 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/multiIntersectBed - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/multiIntersectBed - from package: BEDTools

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

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