Actually will not be the same. unaligned_dirs[0], will be Unaligned_* (i.e Unaligned_6bp). With these first cases I create the structure for the merging results, and I keep passing and overwriting the merge_dir (notice that I pass it in every following call). If I did like you say, I'll be overwriting one (the firs one concretely) of the results folders. Right?