windowBed: 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/windowBed - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/windowBed - from package: BEDTools

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

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