genomeCoverageBed: 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/genomeCoverageBed - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/genomeCoverageBed - from package: BEDTools

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

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