Issue with misalignment correction

[Ryan Abdella]

Hi all,

I'm running into an issue where spIsoNet does not run during relion refine, here is the command :

`which relion_refine_mpi` --o Refine3D/job001/run --auto_refine --split_random_halves --i P25_J323.star --ref J323_000_volume_map.mrc --firstiter_cc --ini_high 30 --dont_combine_weights_via_disc --pool 3 --pad 1  --ctf --particle_diameter 250 --flatten_solvent --zero_mask --solvent_mask J323_008_volume_mask_refine.mrc --solvent_correct_fsc  --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --sym C2 --low_resol_join_halves 40 --norm --scale  --j 2 --gpu "0:1" --external_reconstruct  --pipeline_control Refine3D/job001/

run.err contains this message immediately upon job start:

No protocol specified

Refinement properly proceeds through iterations but I don't see any additional output when the external refinement should run.

I've confirmed these variables are set:

echo $CONDA_ENV

spisonet

echo $RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE

python /home/cryosparc_user/Downloads/spIsoNet-main/spIsoNet/bin/relion_wrapper.py

Any help is greatly appreciated!

[YUNTAO LIU]

Hi Ryan,

I may need more information to diagnose.

1. whether RELION can run successfully without external_reconstruct.

2. whether spIsoNet anisotropy correction can be executed successfully without RELION.

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Best Regards,

Yuntao Liu,  Postdoc.

California NanoSystem Institute

University of California Los Angeles

[YUNTAO LIU]

Hi Ryan,

I believe the "No protocol specified" is not relevant to spIsoNet. Please see here "https://github.com/3dem/relion/issues/307"

Also in your run.out, whether it has something similar to 

" + Making system call for external reconstruction: python /home/cii/software/spIsoNet/bin/relion_wrapper.py Refine3D/job109/run_it001_half1_class001_external_reconstruct.star"