nmds.py: command not found

Have You tried accessing the binary with the full path?

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH

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/nmds.py - from package: qiime

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