bedpeToBam: 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/bedpeToBam - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/bedpeToBam - from package: BEDTools

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

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