Hi @vperetroukhin and thank you for your reply! 
I am using the particles from ab-initio reconstruction as input for the 3D classification, and in this run I have not added a volume. However I have tried to also run it with “input” (also adding a volume). I do the same thing with and without downsampling the particles, but it seems to only work with the downsampled ones.
After waiting around 24hrs the 3D classification fail for the not-downsampled particles unfortunately. It is “failing” after all of the iterations are done (please see picture under “Final”).
This is how the first and final iteration looks like, the final one is right before the error message pasted in my first post.
First:
Final:
