prep_reads: 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/prep_reads - from package: tophat

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

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