bwa: 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/bwa - from package: bwa

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

On Debian possible default full paths are:

/usr/bin/bwa - from package: bwa

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

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