compare_distance_matrices.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/compare_distance_matrices.py - from package: qiime

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

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