make_phylogeny.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/make_phylogeny.py - from package: qiime

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

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