No exposures exported from CS live session

CryoSPARC Live
1

Hi there,

we have two CS instances on campus, one coupled to our Krios for CS live and one for processing. The Krios instance reads in the eer files, and then writes out the data to a network share. I then detached the project from the krios instance and attached the session to the processing instance.

When I open the CS live session in the new instance, it looks like this:

image
image470×1426 81.8 KB

However, the thumbnail previews and all stats are not being displayed:
image
image4592×2464 341 KB

When I export the exposures, I get:

[CPU:   91.3 MB  Avail:  66.18 GB]
Job J8 Started

[CPU:   91.3 MB  Avail:  66.18 GB]
Master running v4.7.1, worker running v4.7.1

[CPU:   92.0 MB  Avail:  66.18 GB]
Working in directory: /groups/plaschka/shared/data/em/Krios/20240809_RPB3_Benzo/cryosparc/CS-mkv7-20250804-144351-eer/J8

[CPU:   92.0 MB  Avail:  66.18 GB]
Running on lane None

[CPU:   92.0 MB  Avail:  66.18 GB]
Resources allocated: 

[CPU:   92.0 MB  Avail:  66.18 GB]
  Worker:  imp-cryosparc-1.vbc.ac.at

[CPU:   92.0 MB  Avail:  66.18 GB]
--------------------------------------------------------------

[CPU:   92.0 MB  Avail:  66.18 GB]
Importing job module for job type export_live_exposures...

[CPU:  226.5 MB  Avail:  66.11 GB]
Job ready to run

[CPU:  226.5 MB  Avail:  66.11 GB]
***************************************************************

[CPU:  226.5 MB  Avail:  66.11 GB]
Started exposures export from cryoSPARC Live P660 S1

[CPU:  226.5 MB  Avail:  66.11 GB]
Acceptance thresholds that are set in Live session:

[CPU:  226.5 MB  Avail:  66.11 GB]
	Max In-Frame Motion - Min: 0.0 -> Max: 5.724

[CPU:  226.5 MB  Avail:  66.11 GB]
	CTF Fit (A) - Min: -2.49 -> Max: 7.329

[CPU:  226.5 MB  Avail:  66.11 GB]
	Median Blob Pick Score - Min: 0.116 -> Max: 0.415

[CPU:  226.5 MB  Avail:  66.11 GB]
In the session, 0 micrographs are manually rejected.

[CPU:  226.5 MB  Avail:  66.11 GB]
------------------------------

[CPU:  226.5 MB  Avail:  66.11 GB]
Exporting all exposures across entire session

[CPU:  226.8 MB  Avail:  66.11 GB]
Exporting 0 matching exposures

[CPU:  227.3 MB  Avail:  66.11 GB]
------------------------------

[CPU:  227.3 MB  Avail:  66.11 GB]
Exporting accepted exposures across entire session

[CPU:  227.3 MB  Avail:  66.11 GB]
Exporting 0 matching exposures

[CPU:  227.3 MB  Avail:  66.11 GB]
------------------------------

[CPU:  227.3 MB  Avail:  66.11 GB]
Exporting rejected exposures across entire session

[CPU:  227.3 MB  Avail:  66.11 GB]
Exporting 0 matching exposures

[CPU:  227.3 MB  Avail:  66.11 GB]
------------------------------

[CPU:  227.3 MB  Avail:  66.11 GB]
Exporting manual_rejected exposures across entire session

[CPU:  227.3 MB  Avail:  66.11 GB]
Exporting 0 matching exposures

[CPU:  227.3 MB  Avail:  66.11 GB]
--------------------------------------------------------------

[CPU:  227.3 MB  Avail:  66.11 GB]
Compiling job outputs...

[CPU:  228.6 MB  Avail:  66.11 GB]
Updating job size...

[CPU:  228.6 MB  Avail:  66.11 GB]
Exporting job and creating csg files...

[CPU:  228.6 MB  Avail:  66.11 GB]
***************************************************************

[CPU:  228.6 MB  Avail:  66.11 GB]
Job complete. Total time 0.36s

The same workflow usually works just fine. Any ideas what might be going wrong and how to troubleshoot?

Thanks in advance, Matthias

2

@mvorlaender What is the version of the second CryoSPARC instance (the one not at the Krios)? CryoSPARC v4.7 included a fix that may be relevant for this problem.
Update: I just realized that you are already running the latest version (v4.7.1) of CryoSPARC.
I will check with our time what additional information might be useful to capture and post here.

1 Like