Empty Tiles during generating tiles

[zsoooc]

I have a problem while generating tiles with generate_tiles.py. It writes randomly "empty tiles" on the log during the process (zoom level 15). It seems that it is totally random and not connected to a geographic area (I loaded a full country pbf to postgis, and now generate tile to a subset). I use a slow hard disk, and run the Ubuntu on VM with more than 6 GB RAM, but it use only 2 CPU core (an old AMD Athlon X3). I checked these tiles and they are really empty.
Screenshot:
click here