fastaq_count_sequences: 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 Debian possible default full paths are:

/usr/bin/fastaq_count_sequences - from package: fastaq

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

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