bp_search2gff: 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_search2gff - from package: bioperl

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

Error in other languages:
bp_search2gff: bevel nie gevind nie
bp_search2gff: comandă negăsită
bp_search2gff: comando não encontrado
bp_search2gff: commande introuvable
bp_search2gff: command not found
bp_search2gff: käsku ei ole
bp_search2gff: không tìm thấy lệnh
bp_search2gff: komanda nerasta
bp_search2gff: Kommando nicht gefunden.
bp_search2gff: kommandot finns inte
bp_search2gff: komut yok
bp_search2gff: nie znaleziono polecenia
bp_search2gff: níor aimsíodh an t-ordú
bp_search2gff: no se encontró la orden
bp_search2gff: no s'ha trobat l'ordre
bp_search2gff: opdracht niet gevonden
bp_search2gff: parancs nem található
bp_search2gff: perintah tidak ditemukan
bp_search2gff: príkaz nenájdený
bp_search2gff: příkaz nenalezen
bp_search2gff: команда не найдена
bp_search2gff: командата не е открита
bp_search2gff: 命令找不到
bp_search2gff: コマンドが見つかりません