multiBamCov: 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/multiBamCov - from package: BEDTools

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

On Debian possible default full paths are:

/usr/bin/multiBamCov - from package: BEDTools

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

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