mergeBed: 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/mergeBed - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/mergeBed - from package: BEDTools

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

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