bed12ToBed6: 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/bed12ToBed6 - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/bed12ToBed6 - from package: BEDTools

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

Error in other languages:
bed12ToBed6: bevel nie gevind nie
bed12ToBed6: comandă negăsită
bed12ToBed6: comando não encontrado
bed12ToBed6: commande introuvable
bed12ToBed6: command not found
bed12ToBed6: käsku ei ole
bed12ToBed6: không tìm thấy lệnh
bed12ToBed6: komanda nerasta
bed12ToBed6: Kommando nicht gefunden.
bed12ToBed6: kommandot finns inte
bed12ToBed6: komut yok
bed12ToBed6: nie znaleziono polecenia
bed12ToBed6: níor aimsíodh an t-ordú
bed12ToBed6: no se encontró la orden
bed12ToBed6: no s'ha trobat l'ordre
bed12ToBed6: opdracht niet gevonden
bed12ToBed6: parancs nem található
bed12ToBed6: perintah tidak ditemukan
bed12ToBed6: príkaz nenájdený
bed12ToBed6: příkaz nenalezen
bed12ToBed6: команда не найдена
bed12ToBed6: командата не е открита
bed12ToBed6: 命令找不到
bed12ToBed6: コマンドが見つかりません