Clean up code + terminal output

[mikolmogorov]

Remove commented out code, or code that is never used - unless these is a god reason to keep it.

Comment out the terminal/log output that is no longer necessary, but do keep the useful debug output (in case something goes wrong with other user's runs).

[microbemarsh]

Since this is undoubtedly going to get some popularity, the conda install in the read.me should be make -C submodules/Flye instead of make -C submodules/flye with the current naming conventions of the package.

[mikolmogorov]

@microbemarsh oups, thanks for pointing that out - fixed!

[katerinakazantseva]

@fenderglass done, I also changed console logging level to INFO (file logging still have DEBUG level), to avoid excessive information