After updating to V3.0, Patch CTF estimation error: Axis limits cannot be NaN or Inf

Troubleshooting
1

Dear cryoSPARC users,
I updated cryoSPARC v2.14.3 to v3.0.0 successfully and then tried to run Patch CTF estimation job but it had errors as following:

[CPU: 254.1 MB]  Traceback (most recent call last):
  File "cryosparc_worker/cryosparc_compute/run.py", line 84, in cryosparc_compute.run.main
  File "cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py", line 344, in cryosparc_compute.jobs.ctf_estimation.run.run
  File "/home/boland/software/cryosparc2/cryosparc2_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/matplotlib/pyplot.py", line 1586, in ylim
    ret = ax.set_ylim(*args, **kwargs)
  File "/home/boland/software/cryosparc2/cryosparc2_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/matplotlib/axes/_base.py", line 3568, in set_ylim
    bottom = self._validate_converted_limits(bottom, self.convert_yunits)
  File "/home/boland/software/cryosparc2/cryosparc2_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/matplotlib/axes/_base.py", line 3214, in _validate_converted_limits
    raise ValueError("Axis limits cannot be NaN or Inf")
ValueError: Axis limits cannot be NaN or Inf


[CPU: 606.2 MB]  Traceback (most recent call last):
  File "/home/boland/software/cryosparc2/cryosparc2_worker/cryosparc_compute/jobs/runcommon.py", line 1711, in run_with_except_hook
    run_old(*args, **kw)
  File "/home/boland/software/cryosparc2/cryosparc2_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/threading.py", line 870, in run
    self._target(*self._args, **self._kwargs)
  File "/home/boland/software/cryosparc2/cryosparc2_worker/cryosparc_compute/jobs/pipeline.py", line 164, in thread_work
    work = processor.process(item)
  File "cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py", line 209, in cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
AssertionError: Job is not in running state - worker thread with PID 21525 terminating self.

Any ideas about this error? Any input will be greatly valued. Thank you in advance!

2

Hi @YuJun,

Did this error happen immediately upon starting the job, or were some micrographs first processed successfully?
Can you also provide your OS version?

3

@apunjani, I’m seeing the same issue on 2 different computers after updating to v3.0.1. Both are running centos7. One has 4 1080Tis and the other has 2 3090s. The micrographs were motion corrected in Warp and imported into cryosparc. The job fails immediately with the above error. Any thoughts?

Edit: I’ve used the workstation with 4x 1080Tis previously to import motion corrected micrographs and done the CTF (all the way to a 3A structure) with v3.0.1 so I am not sure why it is failing this time around.

4

So, CTFFind seems to be working on the imported micrographs but not Patch CTF. Seems a little odd.

5

Hi,
So sorry to reply to you so late. Actually , I figured the problem out. I checked the microscope parameters and found that I set the Cs to 0.00(the microscope is Cs corrected). After setting Cs to 0.01, then everything is fine. Both the CTF patch and Gctf are working.

Jun

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