Retraining last layer of inception
I'm running the script now.   It's just creating bottleneck files for the flowers images, i.e. the old bottleneck files are not present.

You can see that the bottleneck files are all created in the /tmp directory.

This makes sense as the point of the script is only to retrain the final layer of the network.   The idea is that the previously trained layers will work for an arbitrary set of images.