Patch CTF estimate failed

CTF Estimation
1

Hi I am runining Cryosparc Patch CTF estimate job on cluster. it works at the beginning and failed at the 6th image processing.
error info:

Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 96, in cryosparc_compute.run.main
  File "cryosparc_master/cryosparc_compute/jobs/ctf_estimation/run.py", line 373, in cryosparc_compute.jobs.ctf_estimation.run.run
  File "/home/harper/cryosparc_app/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/matplotlib/pyplot.py", line 1755, in ylim
    ret = ax.set_ylim(*args, **kwargs)
  File "/home/harper/cryosparc_app/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/matplotlib/axes/_base.py", line 4027, in set_ylim
    bottom = self._validate_converted_limits(bottom, self.convert_yunits)
  File "/home/harper/cryosparc_app/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/matplotlib/axes/_base.py", line 3614, in _validate_converted_limits
    raise ValueError("Axis limits cannot be NaN or Inf")
ValueError: Axis limits cannot be NaN or Inf

Screenshot 2023-06-05 at 17.41.48
Screenshot 2023-06-05 at 17.41.482606×480 97.3 KB

2

cryosparc v4.2.1
toggled on classic still report error when processing the 6th-7th image.

3

Try CTFFIND, see if it also crashes on the same image. If so, there may be image corruption. If not, what is your pixel size? Patch CTF really struggles with extremely high mag (<0.4 A/pix) data, although I don’t remember seeing that particular error before.

If CTFFIND works, proceed from there and carry out per-particle defocus refinement as early as feasible.

4

Hi, thanks for your reply and suggestion. I tried CTFFIND, and it works. Also, the PatchCTF error was fixed by applying 2GPU, and 8GB RAM. The previous failure is because I only used 1GPU,8GB RAM.

5

Try: DO NOT transform the “.gain" to ".mrc” by e2proc2d