I am trying to make an effect where a building is burning down or something similar like this:

The problem is that halfway down there are some parts that does not disapear and stay black:
It does not happen in the material preview, just when rendering with cycles. I need cycles because the video has to be VR compatible.
The way I am doing this is as follows. The building has this material:
It has an empty plain axis attached so that when that moves one part of the building uses the given texture, the other one is transparent and there is this fire like effect in the middle.
Any ideas why there are those black artifacts?
So far I tried modifying the values of the different nodes, changing render values and removing the texture.