My steps are almost the same with you, and I also have this warning even if I split a large geotiff data into two. But I found that If the tile_x = 200/tile_y = 200 in my index matches the data, it will report this warning, if the value is greater than data, it will successfully, but the two geo_em_d02.nc data both wrong (all is 17 or 0). Looking forward to your reply.