Thanks for your quick reply,
I tried again to fix the problem as suggested by Thomas but this did not solve the problem.
Actually I have two machines running phenix, one with the old version 1.3, and the other with 1.4-3 version.
With the old version I have also coot, ccp4, and arp-warp, and all things are running without any problem in this machine.
But in the other computer, I don't have arp-warp in it (ccp4 and coot exist also), and everything was running OK until I updated phenix to 1.4-3. But now even if I downgrade it to 1.3, autobuild does not work.
If I compare echo $PATH results from both machines, I can notice that the path in the one with "defected" autobuild is too long.
I will review again my path and try to fix it, or see if there are other recently-installed programs that interfere with phenix.

Thanks

Youssef.