join_paired_ends.py: 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/lib/qiime/bin/join_paired_ends.py - from package: qiime

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

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