hmmscan: 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/hmmscan - from package: hmmer

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

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