FastTree: 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/fasttree - from package: fasttree
/usr/lib/qiime/bin/FastTree - from package: qiime

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

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