pairToBed: 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/pairToBed - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/pairToBed - from package: BEDTools

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

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