rep_sep: 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/seqan/bin/rep_sep - from package: seqan-apps

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

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