bp_mutate: 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/bp_mutate - from package: bioperl

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

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