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Thank you very much for your quick response.

I was using version 5.14.3 and so there must be the problem. I'm going to try to find one newer.

SOLVED: I've compiled the latest version downloaded from this page and every  thing seams right. Now it's working fine, thanks again.

I'm trying to exec FET  from bash on a Ubuntu 12.04 box. The question is if there's any possibility to run the application without a graphical user interface (like the Windows redistributable version with fet-cl.exe program compiled) as the environment where I'm gonna run FET is a ubuntu box without unity, gnome, kde, or any other desktop environment.

Anyway what I need is to be able to run FET as a batch on a Linux environment, by just selecting inputfile and outputdir and letting FET do whatever it needs to do without human intervention. Any possibility?

Thanks in advance.