Error in relion_wrapper.py

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Sacha Sverzhinsky

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Sep 26, 2025, 1:04:05 PM9/26/25
to spIsoNet
Hello, I'm following the tutorial and here is what I'm submitting:
`which relion_refine_mpi` --o Refine3D/job004/run --auto_refine --split_random_halves --i job025_tutorial.star --ref HA_reference.mrc --firstiter_cc --ini_high 10 --dont_combine_weights_via_disc --scratch_dir /localssd/asverzh --pool 30 --pad 2  --ctf --particle_diameter 170 --flatten_solvent --zero_mask --solvent_mask mask.mrc --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --sym C3 --low_resol_join_halves 40 --norm --scale  --j 4 --gpu "" --external_reconstruct --keep_lowres --solvent_correct_fsc --pipeline_control Refine3D/job004/

The external_reconstruct variable was successfully exported: 
echo $RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE
python /usr/local/spIsoNet/spIsoNet/spIsoNet/bin/relion_wrapper.py

Here is the error after the maximization step:
The following warnings were encountered upon command-line parsing:
WARNING: Option --keep_lowres   is not a valid RELION argument
  File "/usr/local/spIsoNet/spIsoNet/spIsoNet/bin/relion_wrapper.py", line 36
    params += f" {mrc1} {mrc2}"
                              ^
SyntaxError:   File "/usr/local/spIsoNet/spIsoNet/spIsoNet/bin/relion_wrapper.py", line 36
    params += f" {mrc1} {mrc2}"
                              ^
SyntaxError: invalid syntax
invalid syntax
in: /tmp/sbgrid/spack-stage/spack-stage-relion-4.0.1-kyu7xkyxlng22wnqvnl4sdrzrfo34czt/spack-src/src/backprojector.cpp, line 1294
ERROR:
 ERROR: there was something wrong with system call: python /usr/local/spIsoNet/spIsoNet/spIsoNet/bin/relion_wrapper.py Refine3D/job004/run_it001_half2_class001_external_reconstruct.star
in: /tmp/sbgrid/spack-stage/spack-stage-relion-4.0.1-kyu7xkyxlng22wnqvnl4sdrzrfo34czt/spack-src/src/backprojector.cpp, line 1294
ERROR:
 ERROR: there was something wrong with system call: python /usr/local/spIsoNet/spIsoNet/spIsoNet/bin/relion_wrapper.py Refine3D/job004/run_it001_half1_class001_external_reconstruct.star
=== Backtrace  ===

I also tried with relion 4.0.0 and without solvent_correct_fsc in additional arguments and I got the same error. 
Thanks for the help!

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