blastdbcp: 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
/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/blastdbcp - from package: ncbi-blast+

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