long_spanning_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/long_spanning_reads - from package: tophat

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

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