cdhit-est-2d: 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-est-2d - from package: cd-hit

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

Error in other languages:
cdhit-est-2d: bevel nie gevind nie
cdhit-est-2d: comandă negăsită
cdhit-est-2d: comando não encontrado
cdhit-est-2d: commande introuvable
cdhit-est-2d: command not found
cdhit-est-2d: käsku ei ole
cdhit-est-2d: không tìm thấy lệnh
cdhit-est-2d: komanda nerasta
cdhit-est-2d: Kommando nicht gefunden.
cdhit-est-2d: kommandot finns inte
cdhit-est-2d: komut yok
cdhit-est-2d: nie znaleziono polecenia
cdhit-est-2d: níor aimsíodh an t-ordú
cdhit-est-2d: no se encontró la orden
cdhit-est-2d: no s'ha trobat l'ordre
cdhit-est-2d: opdracht niet gevonden
cdhit-est-2d: parancs nem található
cdhit-est-2d: perintah tidak ditemukan
cdhit-est-2d: príkaz nenájdený
cdhit-est-2d: příkaz nenalezen
cdhit-est-2d: команда не найдена
cdhit-est-2d: командата не е открита
cdhit-est-2d: 命令找不到
cdhit-est-2d: コマンドが見つかりません