mothur: 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/bin/mothur - from package: mothur

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

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