cd-hit-para: 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/cd-hit-para - from package: cd-hit

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

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