mapBed: 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/mapBed - from package: BEDTools

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

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