clean_checkpoints: 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/lib/fastdnaml/bin/clean_checkpoints - from package: fastdnaml

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

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