sortBed: 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/sortBed - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/sortBed - from package: BEDTools

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

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