Wobbly flight in auto mode

Today I was flying a short mission. After takeoff everything was right. After after few way points it started to wobble. It was close to crash. Mechanically everything looks good. I am using Pixhawk 2 (cube) with Here GNSS.
Could somebody take a look what was wrong?
The log: https://files.fm/u/wnbjtmbh
Thanh you in advance.

Were you fighting wind?
Have you autotuned the hex?
Is it balanced?

There seems to be plenty of power and that might be part of the issue.
The motors are running at different rates for a lot of the time.

Your DesRoll/Pitch is very different from actual.

Just some observations.

Did your problem solved? we are facing similar problem from past few days