Dear @OndrejTrhan,
The alignment is not finished. To expor the .rcalign file, we are running -exportLatestComponents command.
When it comes to selecting the images to be used by RealityCapture, we are planning to do the filtering before importing the images. That is why, I believe that previous question is currently out of scope 
I need to say some words to the picture, I have attached. This picture was generated by us using initial metadata of images. The default color is green. There is no additional information encoded by color. The interesting zone of the image is emphasised by red circle. If you look carefully, you will see the green dots there. These images caused the alignment process to fail. I introduce it as an example, of the pattern, we noticed, that the RealityCapture cannot grasp. We hoped that maybe there are other known patterns
I hope that misunderstanding is solved now.
I am looking forward to your reply.
Best regards,