fastaq_capillary_to_pairs: 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_capillary_to_pairs - from package: fastaq

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

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