Hi Carolina, 

it seems everything is working fine for the ALFF, but something very weird is happening with your subjectlist. Did you happen to create that on a windows machine and then copy it to your virtual machine. Text-encoding from windows to linux sometimes does weird things.

Can you try just making a subjectlist using gedit in the virtual machine?

I'm not sure what is causing the directories to be created. I would first see if we can resolve the weird characther issue...

Maarten