cdhit: 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/cdhit - from package: cd-hit

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

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