Dear users,
I encounter an error while running the Patch CTF job on CryoSPARC. It happened after processing the 4th micrograph.
The error message is as follows:
File “cryosparc_master/cryosparc_compute/run.py”, line 129, in cryosparc_master.cryosparc_compute.run.main File “cryosparc_master/cryosparc_compute/jobs/ctf_estimation/run.py”, line 400, in cryosparc_master.cryosparc_compute.jobs.ctf_estimation.run.run File “/blue/user/apps/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/matplotlib/pyplot.py”, line 1998, in ylim ret = ax.set_ylim(*args, **kwargs) File “/blue/user/apps/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/matplotlib/axes/_base.py”, line 3898, in set_ylim return self.yaxis._set_lim(bottom, top, emit=emit, auto=auto) File “/blue/user/apps/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/matplotlib/axis.py”, line 1210, in _set_lim v0 = self.axes._validate_converted_limits(v0, self.convert_units) File “/blue/user/apps/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/matplotlib/axes/_base.py”, line 3585, in _validate_converted_limits raise ValueError(“Axis limits cannot be NaN or Inf”) ValueError: Axis limits cannot be NaN or Inf
I am an inexperienced user and I was not able to find a way to fix this issue. Any help is greatly appreciated.
Edit:
I was able to solve the issue. I am typing for reference in case it can be useful for anyone.
I took note of the micrograph file name that causes the error message. I made a Curate exposures job and looked up that particular micrograph. It was a completely black image. I manually rejected it then ran the patch CTF job again. It proceeded without an error.