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The motion correction job was run in 4.6, so I am not sure why this error occurred. But I decided to following the instructions and did the following:
run 200 micrograph motion corrections
Use the output from 1 as input for micrograph denoiser run with the goal to generate a model to be used for denoiser job of the failed run.
However, the new denoiser job also failed with a different error (below). I am not sure what I did wrong here.
The outputs of these commands for both the failed Denoiser job and the upstream Patch Motion Correction job
csprojectid=P99 # replace with actual project ID
csjobid=J199 # replace with id of relevant job
cryosparcm cli "get_job('$csprojectid', '$csjobid', 'job_type', 'version', 'created_at', 'started_at', 'status', 'params_spec', 'errors_run', 'input_slot_groups')"
The error messages are below:
For the denoiser after curated exposure
[CPU: 483.3 MB] Traceback (most recent call last): File “cryosparc_master/cryosparc_compute/run.py”, line 129, in cryosparc_master.cryosparc_compute.run.main File “cryosparc_master/cryosparc_compute/jobs/micrograph_analysis/run_denoise.py”, line 97, in cryosparc_master.cryosparc_compute.jobs.micrograph_analysis.run_denoise.run_train AssertionError: Input micrographs do not contain denoiser training data. In order to train a denoiser model specific to this dataset, you must re-run Patch Motion correction on a subset of the movies to produce training data. By default, denoiser training requires only 100 movies with training data. Please run Patch motion correction, setting the “Only process this many movies” parameter to 100, and ensure the “Output denoiser training data” parameter is turned on. Then, connect the resulting micrographs to this job to train a new model. Alternatively, you can use a denoiser model that you have trained on a different data by connecting to the Denoiser model input of this job, or you can turn on the “Use pretrained model” parameter of this job to use a generic pretrained denoiser model, without the need for training data.
For the denoiser after the newly run patch motion:
[CPU: 83.8 MB] Traceback (most recent call last): File “cryosparc_master/cryosparc_compute/run.py”, line 85, in cryosparc_master.cryosparc_compute.run.main File “/cluster/software/cryosparc/cryosparc-itrssyaoxialab/v4.7/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 1223, in check_default_inputs assert False, 'Non-optional inputs from the following input groups and their slots are not connected: ’ + missing_inputs + ‘. Please connect all required inputs.’ AssertionError: Non-optional inputs from the following input groups and their slots are not connected: exposures.ctf. Please connect all required inputs.
I was not able to get a return of the commands. I typed in the following commands in a folder called cryosprac_workers:
The command would have to be run on the CryoSPARC master server. If the admin of the CryoSPARC instance is happy with you running commands on that server, you could call cryosparcm by using its absolute path, like
/path/to/cryosparc_master/bin/cryosparcm ...
Please ask the admin of the CryoSPARC installation
whether the admin is okay with you running the command
