bp_bioflat_index: 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_bioflat_index - from package: bioperl

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

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