I’m getting the following error with v3.0.1 of cryoSPARC when I try to run a patch motion correction job:
[CPU: 225.4 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/motioncorrection/run_patch.py”, line 44, in cryosparc_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi
AttributeError: ‘NoneType’ object has no attribute ‘add_fields’
The number of GPU used was 1. Movies imported were from previous Import movies job and other parameters were left at default.
Usually when we see this error message it means that something went wrong with the upstream import movies job - basically there’s something wrong with the data on disk that patch motion correction is trying to read. Does this happen with all data, or is it only a specific job?
Thank you for the reply. No one else in the lab has reported having this issue and appears to be isolated to patch motion correction I’m running. The import movies job I’m using as an input was done through the clone job option. After reading through more troubleshooting posts, I found one where someone else was getting the same error message doing the template or manual picking using an input on a cloned job. The suggestion made in that post was to rerun the input job and then rerun the job that is giving the error. I have done this and patch motion correction appears to be working just fine now.
It could be that you hit some obscure incompatibility between old jobs (pre v3) and v3 jobs. We’ll keep in eye on it. Glad to hear the issue is resolved.
I am running cryosparc 3.2.0.
I had to rerun a completed patch motion correction job because I used a wrong total dose and wrongly activated phase in the import movie. The job ran but failed midway. So I marked it as completed and try to continue on a new patch motion correction using the micrographs_incompleted as input. The job failed the following error :
IsADirectoryError: [Errno 21] Is a directory [Errno 21] Is a directory: ‘/data2/PNCC/BsaXI_21apr01_C1/P35/’
But the previous PMC job on the same dataset in the same project directory finished without problem. Restart CS doesn’t help.
Please advice. Thanks.
Sorry @hsnyder, it seems the third time is a charm. I start a new continuation PMC job and looks as if it is running
