linksBed: 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/linksBed - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/linksBed - from package: BEDTools

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

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