MapAlignmentEvaluation: 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/MapAlignmentEvaluation - from package: topp

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

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