nhmmer: 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/nhmmer - from package: hmmer

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

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