Encountered a new problem while extracting ~2mil particles from 5k mics (2 GPU, box 420 -> 48) - it got stuck and was hanging on the last micrograph. Killed the job and marked as complete and the output contains no particles. Try to 2D classify or inspect picks and get the error “object of type ‘NoneType’ has no len()”
Final lines of the extract job look like this:
[CPU: 2.01 GB] – 0.0: processing imported/asdf.mrc
Writing to asdf/extract/asdf.mrc
[CPU: 3.01 GB] (5017 of 5021) Finished processing micrograph 5018.
[CPU: 3.01 GB] (5018 of 5021) Finished processing micrograph 5019.
[CPU: 3.01 GB] (5019 of 5021) Finished processing micrograph 5020.
(Hanging here - Kill and mark as complete)
[CPU: 504.8 MB] Finalizing Job…
[CPU: 504.8 MB] Passing through outputs for output group micrographs from input group micrographs
[CPU: 504.8 MB] This job outputted results [‘micrograph_blob’]
[CPU: 504.8 MB] Loaded output dset with 0 items
[CPU: 504.8 MB] Passthrough results [‘mscope_params’, ‘ctf’, ‘ctf_stats’, ‘micrograph_blob_non_dw’]
[CPU: 504.8 MB] Loaded passthrough dset with 5021 items
[CPU: 504.8 MB] Intersection of output and passthrough has 0 items
[CPU: 504.8 MB] Passing through outputs for output group particles from input group particles
[CPU: 504.8 MB] This job outputted results [‘blob’]
[CPU: 504.8 MB] Loaded output dset with 0 items
[CPU: 504.8 MB] Passthrough results [‘location’, ‘ctf’, ‘pick_stats’]
[CPU: 1.57 GB] Loaded passthrough dset with 2143688 items
[CPU: 1.20 GB] Intersection of output and passthrough has 0 items
[CPU: 1.20 GB] Checking outputs for output group micrographs
[CPU: 1.20 GB] Checking outputs for output group particles
[CPU: 1.20 GB] Done
The cloned extraction job ran but it extracted fewer particles than the template picker output.
Template picker : Particle TOTAL ITEMS 2143688, Micrograph TOTAL ITEMS 5021
Extraction : Particle TOTAL ITEMS 1810244, Micrograph TOTAL ITEMS 5021