gtf_juncs: 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/gtf_juncs - from package: tophat

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

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