fastaq_to_mira_xml: command not found

Have You tried accessing the binary with the full path?

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 Debian possible default full paths are:

/usr/bin/fastaq_to_mira_xml - from package: fastaq

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