When the input file was download from windows system, sometimes it may cause probelm.

When come to this kind of problem, the pipeline seems goes well, and produce the Blat results, and the "new_blatout", while not the final KaKs results, with the comparative large problem_locs.log indicate can not open "tmp.fas.txt".

To solve this problem, just tranfer the format to UTF-8.

With Emacs in linux, the process is  C-x C-m f utf-8-unix