nucBed: 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/nucBed - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/nucBed - from package: BEDTools

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

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