Hi:
If you are running your script on Windows, create a batch script that 1) Calls Amares batch script and then 2) kills the command window. The script would look something like:
CALL MyAmaresBatchScript.bat &
taskkill /IM cmd.exe
However, you should be careful in making sure that the AMARES “results” file gets completely written into disk before you “kill” the command line. So I suggest to add some pause before you kill the command line (e.g. 3s pause):
CALL MyAmaresBatchScript.bat &
timeout 3
taskkill /IM cmd.exe