FileVault Conversion message during OS X EI Capitan installtion

Hi All,

I recently bought a customized 13" Retina MBP and since it came with the default user account and home folder name, I decided to change it to the one I wanted as per the instructions givenhere. However, post that the system prompted for a restart which I did but my MB failed to boot up properly. The daisy wheel kept spinning for hours. When I tried restarting, I got the prohibitory or 'No Entry' sign and I was not able to go any further. I later decided to restart in the recovery mode (command + R) using Internet Recovery over Wi-Fi.

I chose to re-install OS X from the available options and selected Macintosh HD (is this where the OS comes pre-installed on a new one??) when it asked for the disk where I wanted to install the OS as per the screenshot below:

The moment this was chosen, the FileVault conversion message came up and the below activity has been going on for hours. As you can see, 166,855 odd lines have gone by (still counting) and there is no sign of this coming to an end.

Luckily, there was nothing to be backed up as the system was new so there's nothing to lose but these messages have started worrying me now. I've no idea how long this is going to take and am not sure if I'll ever be able to launch my OS as before. Has something terribly gone wrong here? Please advise. There have been suggestions on other threads not to disrupt this conversion process (as it might screw up my MB beyond repair) so I've left the system untouched.

Should this be a cause of concern or am I safe in assuming everything will be alright? Please let me know

Many thanks