qualfa2fq.pl: 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/qualfa2fq.pl - from package: bwa

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

Error in other languages:
qualfa2fq.pl: bevel nie gevind nie
qualfa2fq.pl: comandă negăsită
qualfa2fq.pl: comando não encontrado
qualfa2fq.pl: commande introuvable
qualfa2fq.pl: command not found
qualfa2fq.pl: käsku ei ole
qualfa2fq.pl: không tìm thấy lệnh
qualfa2fq.pl: komanda nerasta
qualfa2fq.pl: Kommando nicht gefunden.
qualfa2fq.pl: kommandot finns inte
qualfa2fq.pl: komut yok
qualfa2fq.pl: nie znaleziono polecenia
qualfa2fq.pl: níor aimsíodh an t-ordú
qualfa2fq.pl: no se encontró la orden
qualfa2fq.pl: no s'ha trobat l'ordre
qualfa2fq.pl: opdracht niet gevonden
qualfa2fq.pl: parancs nem található
qualfa2fq.pl: perintah tidak ditemukan
qualfa2fq.pl: príkaz nenájdený
qualfa2fq.pl: příkaz nenalezen
qualfa2fq.pl: команда не найдена
qualfa2fq.pl: командата не е открита
qualfa2fq.pl: 命令找不到
qualfa2fq.pl: コマンドが見つかりません