Select 2D classes - IndexError in v2.14.2

Troubleshooting
1

Hi
After updating v2.14.2, an error occurs in the part where there was no problem before updating.
When running the select 2D classes, the following error code appear.
(Prior to the update, select 2D classes were smooth with the same data)

[CPU: 192.9 MB]  Traceback (most recent call last):
  File "cryosparc2_master/cryosparc2_compute/run.py", line 82, in cryosparc2_compute.run.main
  File "cryosparc2_compute/jobs/select2D/run.py", line 253, in run
    fig_group_included = plotutil.plot_images_simple(particles_included_to_plot[particle_include_idxs[:9]], rows=3, cols=3, radwn=6, figscale=0.6)
IndexError: index 7 is out of bounds for axis 0 with size 7

Other data also have the same kind of error.

[CPU: 207.8 MB]  Traceback (most recent call last):
  File "cryosparc2_master/cryosparc2_compute/run.py", line 82, in cryosparc2_compute.run.main
  File "cryosparc2_compute/jobs/select2D/run.py", line 253, in run
    fig_group_included = plotutil.plot_images_simple(particles_included_to_plot[particle_include_idxs[:9]], rows=3, cols=3, radwn=6, figscale=0.6)
IndexError: index 1 is out of bounds for axis 0 with size 1

[CPU: 192.1 MB]  Traceback (most recent call last):
  File "cryosparc2_master/cryosparc2_compute/run.py", line 82, in cryosparc2_compute.run.main
  File "cryosparc2_compute/jobs/select2D/run.py", line 253, in run
    fig_group_included = plotutil.plot_images_simple(particles_included_to_plot[particle_include_idxs[:9]], rows=3, cols=3, radwn=6, figscale=0.6)
IndexError: index 2 is out of bounds for axis 0 with size 2

I tried forced reinstallation and rebooting but it didn’t help.
I would appreciate it if anyone could let me know what to do.
Thanks

2

I am also running into this error on multiple jobs with different particle sets. Is there a solution other than reverting to an older version?

Thank you,

Ryan

3

Same issue. Is there a way to fix it through the cmd line?

4

Hello All,

I just wanted to jump into the conversation and say that we are also running into this issue when running “Select 2D Classes” after updating. We are running cryoSPARC via GPU cluster, but not sure if this would make a difference. As a reference, here is the error again:

[CPU: 234.3 MB] Traceback (most recent call last):
** File “cryosparc2_master/cryosparc2_compute/run.py”, line 82, in cryosparc2_compute.run.main**
** File “cryosparc2_compute/jobs/select2D/run.py”, line 253, in run**
** fig_group_included = plotutil.plot_images_simple(particles_included_to_plot[particle_include_idxs[:9]], rows=3, cols=3, radwn=6, figscale=0.6)**
IndexError: index 8 is out of bounds for axis 0 with size 8

Hopefully there is a resolution soon! Thanks!!

5

Hi,

Our group updated to the latest version of cryosparc on Feb 24th, 2020. I have run several 2D selection jobs prior to today, and they are all finished successfully. However, when I run 2D selection job today, it failed with the similar error msg indicated in the posts above. I have tried several times, no luck yet.

Here is the full error msg:
[CPU: 1.61 GB] Traceback (most recent call last):
File “cryosparc2_master/cryosparc2_compute/run.py”, line 82, in cryosparc2_compute.run.main
File “cryosparc2_compute/jobs/select2D/run.py”, line 263, in run
fig_group_excluded = plotutil.plot_images_simple(particles_excluded_to_plot[particle_exclude_idxs[:9]], rows=3, cols=3, radwn=6, figscale=0.6)
IndexError: index 1123 is out of bounds for axis 0 with size 1012

Hope this can be resolved soon!

6

Hi,

Just want to give a quick update to what I have posted above.

My 2D classification yields 50 classes. And I have about 30 decent classes I want to select. I accidentally found that if I just remove one class (which is a relatively low resolution class) from my selection, my 2D selection jobs can be finished successfully. I tried to only select that specific problematic class, and the job failed again. So it seems some of the classes (one in my case) cause the failure of 2D selection due to some unknown reasons.

7

Hi @KSJ, @RyanFeathers, @hxn, @bpmahon, @bding

This fix is now included in v2.15.0- if you update to this version, the fix included in the file below is already applied!

See changelog here: https://cryosparc.com/blog/new-in-v2-15

This is definitely a bug, and because of how many users it’s affecting, we’ve uploaded a replacement file that includes the fix for this issue.

Download the file from our AWS S3 bucket here:
https://structura-assets.s3.amazonaws.com/select2d_v2.14_index_error_bugfix/run.py

Download directly or use wget via the command line:

wget https://structura-assets.s3.amazonaws.com/select2d_v2.14_index_error_bugfix/run.py

And replace the file in the following folder on the cryoSPARC master node:
cryosparc2_master/cryosparc2_compute/jobs/select2D/

There is no need to restart cryoSPARC. Once you copy the file you can simply clone/create a new Select 2D job and you should be on your way! Also, future versions of cryoSPARC will include this fix.

Thank you for reporting, and sorry for the inconvenience.

3 Likes
8

it’s working now!
Thank you :smiley: