Before running the cluster analysis, you need to build the sample unit cell. Click Run new operation | Initialisation | Building, and Accept. (If you have not deleted the structures with higher Distance, choose the Best available fit option.) Click Accept.
Once back in the Operations List screen, click Run new operation... | Initialisation... | Auto Cluster Ratio. Click Run sequence.
After completion, the Auto Cluster analysis will return you to the Operations List screen, ready for to view the characteristics of the simulation as described in the next section.