getOverlap: 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/getOverlap - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/getOverlap - from package: BEDTools

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

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