I just got the same error coming up again in 1.1.0. It happened right when the model switched from using seeds to the nascent model. It could be that none of the documents were relevant after I exhausted the seed list, but wanted to bring it up.
/Users/ahalterman/anaconda3/lib/python3.6/site-packages/prodigy/app.py:60: RuntimeWarning: Mean of empty slice.
tasks = controller.get_questions()
/Users/ahalterman/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:80: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
/Users/ahalterman/anaconda3/lib/python3.6/site-packages/prodigy/app.py:60: RuntimeWarning: Degrees of freedom <= 0 for slice
tasks = controller.get_questions()
/Users/ahalterman/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:105: RuntimeWarning: invalid value encountered in true_divide
arrmean, rcount, out=arrmean, casting='unsafe', subok=False)
/Users/ahalterman/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:127: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)