bedToBam: 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/bedToBam - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/bedToBam - from package: BEDTools

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

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