masai_output_pe: 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/masai_output_pe - from package: seqan-apps
/usr/lib/seqan/bin/masai_output_pe - from package: seqan-apps

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

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