Error in Extracting from Micrographs after inspect Picks

Particle Picking
1

Hello,
I am trying to extract particles from micrographs and succeed, but I found two errors:

1.No output result match for micrographs.micrograph_blob_denoised in job.
2.Passthrough result micrograph_blob_denoised not found in dataset - removing the slot from output results.

The consequence is the further job 2D classification cannot work ,it raised errors as following:
AssertionError: CTF parameters must be connected to perform CTF correction.

I assume that the issue happened since the output of the extracting from micrographs didn’t include CTF parameters but I use the Patch CTF estimated micrographs as input in Extraction job.

CryoSPARC v4
Thanks a lot

2

Welcome to the forum @yanning.

For the job(s) where you observed

please can you post the outputs of these commands

csprojectid=P99 # replace with actual project ID
csjobid=J199 # replace with relevant job's ID
cryosparcm cli "get_job('$csprojectid', '$csjobid', 'job_type', 'version', 'status',  'params_spec', 'errors_run', 'input_slot_groups')"
cryosparcm eventlog $csprojectid $csjobid | tail -n 50

Please can you also post a screenshot of a portion of the job tree that includes all the jobs that you mentioned in your post and shows the relevant jobs’ IDs and job types.

3

@yanning did you extract from denosied micrographs ? The picks between donoised and regular micrographs should translate e.g. if you blob pick on denoised, inspect picks, junk filter, then extract those particles from the patchCTF micrographs.

4

Hi , thanks for responding，it works now,but actually I didn’t find solution.
I just created a new same job for Extracting from Micrographs, and use the new output for further job, but the original job still has error when I try to restart the job.

Thanks again.
best,
Yan

5

Hi , thanks for responding, it works now.
I did extract the particles from the patchCTF micrographs, but the CTF parameters got lost in the output of Extracting from Micrographs. I still haven’t been able to solve this problem and I had to create a new job.

Thanks again.
Best,
Yan

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