Misalignment correction errors out after 10th iteration

[William Nicolas]

Hello Yuntao,

We are trying to run misalignment correction trough SBgrid on our HPC. By following your instructions on the tutorial, and using the attached run_submit.script, we are able to run the refinement process. However, it errors out, seemingly at the end of the process (see run.out and run.err). Run.out shows that it is able to start the external_reconstruct and succesfully run it, multiple times, however at the end, it says the following:

 eval "$(conda shell.bash hook)" && conda activate spisonet &&  spisonet.py whitening  Refine3D/job045/run_it010_half1_class001_unfil.mrc -o Refine3D/job045/run_it010_half1_class001_unfil.mrc --mask Import/job003/J377_004_volume_mask_refine.mrc --high_res 3.395454 --low_res 10
 eval "$(conda shell.bash hook)" && conda activate spisonet &&  spisonet.py whitening  Refine3D/job045/run_it010_half2_class001_unfil.mrc -o Refine3D/job045/run_it010_half2_class001_unfil.mrc --mask Import/job003/J377_004_volume_mask_refine.mrc --high_res 3.395454 --low_res 10

 RELION version: 5.0-beta-3-commit-ad0c1f
 exiting with an error ...

We try comparing our outputs with the ones you show in your tutorial and we noticed some weird things, like the multiple lines mentioning the pixel size....

We have the spisonet conda environment set up and I have a feeling, because of the run.err lines "EnvironmentNameNotFound: Could not find conda environment: spisonet"

I tried running an interactive session on one of our GPU nodes and I am able to activate the spisonet environment...

Do you see anything fishy in those logs?

Thank you,

William J Nicolas