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

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

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