Hi Juha, Hi Serban,

I was trying to perform a localised reconstruction on my virus particles based off of the mini-tutorial on the wiki. I ran the program with the follwoing parameters:

scipion run relion_localized_reconstruction.py Refine3D/job015/run_ct3_data.star --prepare_particles --create_subparticles --extract_subparticles --sym I1 --vector 0.000,0.618,1.000 --length 80 --angpix 1.065 --particle_size 350 --subparticle_size 80  --j 8 --np 4 --output Particles

while the program sucessfully created a Particles folder with several thousand mrc files it exited with the follwoing error:

Creating subparticles...

~~~~** Running command: relion_refine --sym I1 --print_symmetry_ops --o ./ > relion_symops.tmp

The following errors were encountered upon command-line parsing:

ERROR: Argument --i not found or invalid argument

ERROR:

Errors encountered on the command line (see above), exiting...

File: /programs/x86_64-linux/scipion/1.2/software/em/relion-2.1/src/ml_optimiser.cpp line: 1286

Traceback (most recent call last):

  File "/programs/x86_64-linux/scipion/1.2/software/em/localrec-1.2.0/relion_localized_reconstruction.py", line 252, in <module>

    LocalizedReconstruction().main()

  File "/programs/x86_64-linux/scipion/1.2/software/em/localrec-1.2.0/relion_localized_reconstruction.py", line 206, in main

    symmetry_matrices = matrix_from_symmetry(args.sym)

  File "/programs/x86_64-linux/scipion/1.2/software/em/localrec-1.2.0/lib/localrec/matrix3.py", line 150, in matrix_from_symmetry

    relion_create_symmetry_ops_file(symString, tmpSymFile)

  File "/programs/x86_64-linux/scipion/1.2/software/em/localrec-1.2.0/lib/localrec/matrix3.py", line 160, in relion_create_symmetry_ops_file

    runProgram('relion_refine', '--sym %s --print_symmetry_ops --o ./ > %s' % (symString, filename))

  File "/nfs/sbgrid/programs/x86_64-linux/scipion/1.2/pyworkflow/em/__init__.py", line 185, in runProgram

    pwutils.runJob(None, program, params, env=env)

  File "/nfs/sbgrid/programs/x86_64-linux/scipion/1.2/pyworkflow/utils/process.py", line 51, in runJob

    return runCommand(command, env, cwd)

  File "/nfs/sbgrid/programs/x86_64-linux/scipion/1.2/pyworkflow/utils/process.py", line 65, in runCommand

    check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr, env=env, cwd=cwd)

  File "/nfs/sbgrid/programs/x86_64-linux/scipion/1.2/software/lib/python2.7/subprocess.py", line 186, in check_call

    raise CalledProcessError(retcode, cmd)

subprocess.CalledProcessError: Command 'relion_refine --sym I1 --print_symmetry_ops --o ./ > relion_symops.tmp' returned non-zero exit status 1

I tried to rerun the program with a --create_star flag, but it seems this function has been deprecated in the latest version of the program.
Could you please help me with figuring out how i can work around this error?

Cheers,

Pranav

--

Pranav Shah

Postdoctoral Research Fellow.

Hogle Lab
Harvard Medical School
240 Longwood Avenue
Boston, MA 02115
(617) 432-4360 (fax)
(617) 432-3839 (lab)

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