tophat2: 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/tophat2 - from package: tophat

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

Error in other languages:
tophat2: bevel nie gevind nie
tophat2: comandă negăsită
tophat2: comando não encontrado
tophat2: commande introuvable
tophat2: command not found
tophat2: käsku ei ole
tophat2: không tìm thấy lệnh
tophat2: komanda nerasta
tophat2: Kommando nicht gefunden.
tophat2: kommandot finns inte
tophat2: komut yok
tophat2: nie znaleziono polecenia
tophat2: níor aimsíodh an t-ordú
tophat2: no se encontró la orden
tophat2: no s'ha trobat l'ordre
tophat2: opdracht niet gevonden
tophat2: parancs nem található
tophat2: perintah tidak ditemukan
tophat2: príkaz nenájdený
tophat2: příkaz nenalezen
tophat2: команда не найдена
tophat2: командата не е открита
tophat2: 命令找不到
tophat2: コマンドが見つかりません