uchime: 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/bin/uchime - from package: mothur

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