bp_search2alnblocks: command not found

Have You tried accessing the binary with the full path?

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH

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_search2alnblocks - from package: bioperl

You may install the required package with command apt-get install {package}
Error in other languages:
bp_search2alnblocks: bevel nie gevind nie
bp_search2alnblocks: comandă negăsită
bp_search2alnblocks: comando não encontrado
bp_search2alnblocks: commande introuvable
bp_search2alnblocks: command not found
bp_search2alnblocks: käsku ei ole
bp_search2alnblocks: không tìm thấy lệnh
bp_search2alnblocks: komanda nerasta
bp_search2alnblocks: Kommando nicht gefunden.
bp_search2alnblocks: kommandot finns inte
bp_search2alnblocks: komut yok
bp_search2alnblocks: nie znaleziono polecenia
bp_search2alnblocks: níor aimsíodh an t-ordú
bp_search2alnblocks: no se encontró la orden
bp_search2alnblocks: no s'ha trobat l'ordre
bp_search2alnblocks: opdracht niet gevonden
bp_search2alnblocks: parancs nem található
bp_search2alnblocks: perintah tidak ditemukan
bp_search2alnblocks: príkaz nenájdený
bp_search2alnblocks: příkaz nenalezen
bp_search2alnblocks: команда не найдена
bp_search2alnblocks: командата не е открита
bp_search2alnblocks: 命令找不到
bp_search2alnblocks: コマンドが見つかりません