Particle refinement merge step fails (invalid value encountered in divide)

[JuhaHuiskonen]

My particle refinement is failing at the very end of the merge step with the following error. Any suggestions?

209	Merge3D: Normal termination
210	
211	
212	2024-02-11 19:06:48 [INFO] pyp/refine/frealign/frealign.py:57 | Merge3d took: 00h 00m 28s
213	2024-02-11 19:06:48 [INFO] pyp/refine/csp/particle_cspt.py:57 | Function with merge3d took: 00h 10m 23s
214	2024-02-11 19:06:48 [INFO] pyp/refine/csp/particle_cspt.py:57 | Run parallel reconstruction took: 00h 10m 23s
215	2024-02-11 19:06:48 [INFO] pyp/refine/csp/particle_cspt.py:57 | Total time elapsed: 00h 10m 35s
216	/opt/pyp/src/pyp/refine/frealign/frealign.py:2905: RuntimeWarning: Mean of empty slice.
217	  montage[i * nz : (i + 1) * nz, j * nz : (j + 1) * nz] = (I - I.mean()) / I.std()
218	/usr/local/envs/pyp/lib/python3.8/site-packages/numpy/core/_methods.py:192: RuntimeWarning: invalid value encountered in divide
219	  ret = ret.dtype.type(ret / rcount)
220	/usr/local/envs/pyp/lib/python3.8/site-packages/numpy/core/_methods.py:269: RuntimeWarning: Degrees of freedom <= 0 for slice
221	  ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
222	/usr/local/envs/pyp/lib/python3.8/site-packages/numpy/core/_methods.py:226: RuntimeWarning: invalid value encountered in divide
223	  arrmean = um.true_divide(arrmean, div, out=arrmean,
224	/usr/local/envs/pyp/lib/python3.8/site-packages/numpy/core/_methods.py:261: RuntimeWarning: invalid value encountered in divide
225	  ret = ret.dtype.type(ret / rcount)
226	Traceback (most recent call last):
227	  File "/opt/pyp/bin/run/pyp", line 3955, in <module>
228	    csp_merge(parameters)
229	  File "/opt/pyp/bin/run/pyp", line 2503, in csp_merge
230	    particle_cspt.run_merge(path)
231	  File "/opt/pyp/src/pyp/utils/timer.py", line 78, in wrapper_timer
232	    return func(*args, **kwargs)
233	  File "/opt/pyp/src/pyp/refine/csp/particle_cspt.py", line 1283, in run_merge
234	    csp_class_merge(class_index=1, input_dir=input_dir)
235	  File "/opt/pyp/src/pyp/refine/csp/particle_cspt.py", line 1855, in csp_class_merge
236	    run_mpi_reconstruction(ref, pattern, dataset_name, iteration, mp, fp, input_dir, orderings)
237	  File "/opt/pyp/src/pyp/utils/timer.py", line 78, in wrapper_timer
238	    return func(*args, **kwargs)
239	  File "/opt/pyp/src/pyp/refine/csp/particle_cspt.py", line 1187, in run_mpi_reconstruction
240	    frealign.merge_reconstructions(mp, iteration, ref)
241	  File "/opt/pyp/src/pyp/utils/timer.py", line 78, in wrapper_timer
242	    return func(*args, **kwargs)
243	  File "/opt/pyp/src/pyp/refine/frealign/frealign.py", line 2667, in merge_reconstructions
244	    mreconstruct_post(mp, mp, i, ref, scratch, reclogfile)
245	  File "/opt/pyp/src/pyp/refine/frealign/frealign.py", line 3292, in mreconstruct_post
246	    lim = build_map_montage( scratch + name + ".mrc", radius, "../maps/%s_map.png" % name )
247	  File "/opt/pyp/src/pyp/refine/frealign/frealign.py", line 2905, in build_map_montage
248	    montage[i * nz : (i + 1) * nz, j * nz : (j + 1) * nz] = (I - I.mean()) / I.std()
249	ValueError: could not broadcast input array from shape (0,0) into shape (64,64)
250	2024-02-11 19:06:48 [ERROR] /opt/pyp/bin/run/pyp:3972 | PYP (cspmerge) failed
251	/usr/local/envs/pyp/lib/python3.8/site-packages/numpy/core/fromnumeric.py:3464: RuntimeWarning: Mean of empty slice.
252	  return _methods._mean(a, axis=axis, dtype=dtype,
253	/usr/local/envs/pyp/lib/python3.8/site-packages/numpy/core/_methods.py:192: RuntimeWarning: invalid value encountered in scalar divide
254	  ret = ret.dtype.type(ret / rcount)
255