unionBedGraphs: command not found

Have You tried accessing the binary with the full path?

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/unionBedGraphs - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/unionBedGraphs - from package: BEDTools

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