2D classification error

Troubleshooting
1

Hi cryoSPARC team,

I am using the latest version cryoSPARC v2. With my cryo dataset, I extracted particles from 10 micrographs and I could run 2D classification successfully. However, the 2D classification failed at the first iteration if I extract all of the particles (about 400k) from the same dataset with the exact same settings. The input is the particles from the extraction job. And the only non-default parameters that I changed was the number of classes.

I got all black classes and the following error message for 2D classification:

Iteration 1

– Effective number of classes per image: min nan | 25-pct nan | median nan | 75-pct nan | max nan

– Probability of best class per image: min nan | 25-pct nan | median nan | 75-pct nan | max nan

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_worker/cryosparc2_compute/jobs/class2D/run.py”, line 453, in cryosparc2_compute.jobs.class2D.run.run_class_2D
File “cryosparc2_compute/plotutil.py”, line 830, in plot_hist
ax.hist(vals,bins=bins,range=range, normed=normed, cumulative=cumulative)
File “/home/cryosparc/cryosparc-software/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/matplotlib/init.py”, line 1812, in inner
return func(ax, *args, **kwargs)
File “/home/cryosparc/cryosparc-software/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/matplotlib/axes/_axes.py”, line 6010, in hist
m, bins = np.histogram(x[i], bins, weights=w[i], **hist_kwargs)
File “/home/cryosparc/cryosparc-software/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py”, line 505, in histogram
‘range parameter must be finite.’)
ValueError: range parameter must be finite.

2

Hi @Chen,

Could you provide a bit more info about the dataset? What was the box size, pixel size, etc? Do you have any reason to suspect that some micrographs are completely empty or that the files could be corrupt? What did you use to perform motion correct/CTF estimation?

Thanks,
Ali

3

Hello Ali,

Thank you for your reply. I think it is related to the status of the computer. With the exact same job settings, I could run it successfully the day after I posted the error. However, it is still hard to rationalize because it doesn’t seem to be a memory error.

Here are the information of my dataset:
motion correction: relion implemented motioncor2
CTF estimation: CTFFIND4 in relion
box size: 128
pixel size: 2.18

After I imported the RELION extracted particles into cryosparc, I run the 2D classification of all the imported particles and that is where it failed. Some of the imported particles are completly black because I collected the dataset with the gold grid.

Thanks,
Chen