>Hello,
>I try to run SAMOVA2.0 with Y chromosome DNA data to find out if there is a geographic structure in my dataset. 

>I can't manage to run the program. It yields an error, which you can find below.
>###
>Comparing input files
>      1 [main] arlecore35_first 14480 find_fast_cwd: WARNING: Couldn't compute FAST_CWD pointer.  Please report this problem to
>the public mailing list cygwin@cygwin.com
>Opening Project...
>Arlecore terminated gracefully
>###
>Can you please tell what can be the problem?
>Best,Hovhannes

https://cygwin.com/faq.html#faq.using.fixing-find_fast_cwd-warnings