nhmmscan: 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/nhmmscan - from package: hmmer

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

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