maq2sam-short: 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/maq2sam-short - from package: samtools

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

Error in other languages:
maq2sam-short: bevel nie gevind nie
maq2sam-short: comandă negăsită
maq2sam-short: comando não encontrado
maq2sam-short: commande introuvable
maq2sam-short: command not found
maq2sam-short: käsku ei ole
maq2sam-short: không tìm thấy lệnh
maq2sam-short: komanda nerasta
maq2sam-short: Kommando nicht gefunden.
maq2sam-short: kommandot finns inte
maq2sam-short: komut yok
maq2sam-short: nie znaleziono polecenia
maq2sam-short: níor aimsíodh an t-ordú
maq2sam-short: no se encontró la orden
maq2sam-short: no s'ha trobat l'ordre
maq2sam-short: opdracht niet gevonden
maq2sam-short: parancs nem található
maq2sam-short: perintah tidak ditemukan
maq2sam-short: príkaz nenájdený
maq2sam-short: příkaz nenalezen
maq2sam-short: команда не найдена
maq2sam-short: командата не е открита
maq2sam-short: 命令找不到
maq2sam-short: コマンドが見つかりません