complementBed: 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/complementBed - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/complementBed - from package: BEDTools

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

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