Hello, I’m processing my sample with symmetry enforced, followed by symmetry expansion and local refinement using a mask over one of the protomers. Then this goes through 3D classification where I pool similar classes and run local refinement on them. This has been working flawlessly until one Local Refine job that gives me cFAR: NAN, despite great pose distribution and resolution. I ran a Check Particles job on the same particles and no corruption was detected. Any ideas?
@AlekS Please can you also post
- the CryoSPARC version
- text of the full error trace, and some preceding lines from the log for context
It’s version 4.6.2 and here are some suspicious lines from the log:
/data/cryosparc/cryosparc_worker_obelix/cryosparc_compute/sigproc.py:656: FutureWarning: `rcond` parameter will change to the default of machine precision times ``max(M, N)`` where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass `rcond=None`, to keep using the old, explicitly pass `rcond=-1`.
x = n.linalg.lstsq(w.reshape((-1,1))*A, w*b)[0]
/data/cryosparc/cryosparc_worker_obelix/cryosparc_compute/plotutil.py:571: RuntimeWarning: divide by zero encountered in log
logabs = n.log(n.abs(fM))
/data/cryosparc/cryosparc_worker_obelix/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/numpy/core/_methods.py:179: RuntimeWarning: overflow encountered in reduce
ret = umr_sum(arr, axis, dtype, out, keepdims, where=where)
/data/cryosparc/cryosparc_worker_obelix/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/numpy/core/_methods.py:179: RuntimeWarning: invalid value encountered in reduce
ret = umr_sum(arr, axis, dtype, out, keepdims, where=where)
/data/cryosparc/cryosparc_worker_obelix/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/numpy/core/_methods.py:212: RuntimeWarning: overflow encountered in reduce
arrmean = umr_sum(arr, axis, dtype, keepdims=True, where=where)
/data/cryosparc/cryosparc_worker_obelix/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/numpy/core/_methods.py:212: RuntimeWarning: invalid value encountered in reduce
arrmean = umr_sum(arr, axis, dtype, keepdims=True, where=where)
/data/cryosparc/cryosparc_worker_obelix/cryosparc_compute/plotutil.py:1835: RuntimeWarning: invalid value encountered in subtract
p2 = ax.fill_between(radwns, fsc_mean-std, fsc_mean+std, facecolor='tab:blue', alpha=0.5, label='[+σ, -σ]', zorder=1)
posx and posy should be finite values
posx and posy should be finite values
posx and posy should be finite values
posx and posy should be finite values
posx and posy should be finite values
posx and posy should be finite values
========= sending heartbeat at 2026-07-23 21:29:35.331572
posx and posy should be finite values
posx and posy should be finite values
/data/cryosparc/cryosparc_worker_obelix/cryosparc_compute/plotutil.py:44: RuntimeWarning: invalid value encountered in sqrt
cradwn = n.sqrt(cradwn)
By the way, this project was first processed in version 5.0.6, then detached and attached to an instance with the earlier version. Maybe that could have something to do with it?