annotateBed: 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/annotateBed - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/annotateBed - from package: BEDTools

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

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