gaps: 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/gaps - from package: mummer

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

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