If you know this error
[CPU: 3.84 GB]
Done Full Iteration 42 took 182.430s for 108314 images
[CPU: 3.87 GB]
[CPU: 3.87 GB]
Dropping duplicate particles with worse pick_stats/ncc_score value
[CPU: 3.75 GB]
Traceback (most recent call last):
File "cryosparc_master/cryosparc_compute/run.py", line 95, in cryosparc_master.cryosparc_compute.run.main
File "cryosparc_master/cryosparc_compute/jobs/class2D/run.py", line 555, in cryosparc_master.cryosparc_compute.jobs.class2D.run.run_class_2D
File "/home/groups/brunger/software/cryosparc/cryosparc_worker/cryosparc_compute/geometry.py", line 1051, in remove_duplicate_particles
assert not n.any(n.isclose(0.0, particles['location/micrograph_psize_A'])), "Invalid values (zeroes) detected in location/micrograph_psize_A"
AssertionError: Invalid values (zeroes) detected in location/micrograph_psize_A
Could you provide a bit more information about your workflow? Specifically:
- Which job was used for particle picking and particle extraction?
I used the TopazExtract job for particle picking and extracting from my CTF exposures. All the jobs are done in the Cryosparc. One guess I have is I used the TopazTrain model from my other dataset but the two data sets are of the same data collection parameters and they are the same sample, just collected data in several months difference.
One of our users has just had a similar problem. Their workflow was Live → Template Picker → Extraction → several rounds of 2D Classification/Select 2D.
After I updated to 4.4, they started getting this error:
Could not find micrograph pixel size in particle's locations. Will assume particle image pixel size is equal to micrograph pixel size! Note that if particles were downsampled, this will be false, and remove duplicates will use an incorrect distance scale.
They ran another extraction job in an attempt to remedy this and now get this error:
Traceback (most recent call last): File "cryosparc_master/cryosparc_compute/run.py", line 95, in cryosparc_master.cryosparc_compute.run.main File "cryosparc_master/cryosparc_compute/jobs/class2D/newrun.py", line 467, in cryosparc_master.cryosparc_compute.jobs.class2D.newrun.run_class_2D File "/local_slow/cryosparc/cryosparc_worker/cryosparc_compute/geometry.py", line 1051, in remove_duplicate_particles assert not n.any(n.isclose(0.0, particles['location/micrograph_psize_A'])), "Invalid values (zeroes) detected in location/micrograph_psize_A" AssertionError: Invalid values (zeroes) detected in location/micrograph_psize_A
Yes. Same issue here after upgrading to v4.4
Thank you all. To work around this error immediately, you can run 2D classification jobs with the “remove duplicate particles” parameter disabled. It appears there is incorrectly updated metadata that is causing this issue, which is now preventing remove duplicates from working correctly. I will direct message each of you to request
cs files to help us investigate where the issue is occuring.
I found a new bug. After extracting the particles without binning (box size=288 pix, 1.1A/pix), I ran an Ab-Initio job. The output volume’s volume’s box is 128 pix. And later on, I did the HeteroRefinement, and the FSC drops to ~5.3A, instead of 2.2A ish. So I feel like the invalid values error is still there.
That is normal, not a bug - both these jobs use smaller box sizes for speed
@olibclarke’s comment is right; these jobs downsample the volume internally. I have replied over direct message on the forum, requesting more information regarding the initial bug related to
location/micrograph_psize_A, to help us debug further
After running NU-refinement further, I realized it. Anyway, thank you so much for your fast response!
Any update on that? Reference based motion correction is complaining for duplicate particles and getting killed, but I can run remove duplicates because of that error.
I have followed up with you via direct message on the forum
Hi all (@mokca @CleoShen @dutkap @wxh180),
If anyone has encountered this issue and is willing to share
cs files of the affected particles and micrographs, please contact us on this forum thread, as it would greatly assist in our debugging. Thank you!
Hi @mmclean, Sorry for the late response. What is your email address for sharing the CS files? And what CS files do you need? I have class_averages.cs; particles.cs; passthrough_particles.cs and passthrough_particles_rejected.cs.
Thank you for your response. I have sent you a direct message with these details. You can find the direct message by clicking on your user icon at the top right, and then clicking on the envelope icon. Let me know if you have trouble finding this
CryoSPARC v4.4.1 includes a fix that should prevent remove duplicate particles and 2D Classification from failing with the quoted error:
AssertionError: Invalid values (zeroes) detected in location/micrograph_psize_A. Please let us know if you continue to experience issues in CryoSPARC v4.4.1.