filter_alignment.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/filter_alignment.py - from package: qiime

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

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