Re: [scipion-users] relion 3D auto refinement error (after Bayesian polishing)

[Grigory S. <sha...@gm...>]

Hi Dmitry,

This one is easy. You need to remove brackets from the file name
Runs/064975_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
before import

On Sat, Jul 10, 2021, 15:47 Dmitry A. Semchonok <sem...@gm...> wrote:

> Dear Grigory & colleagues,
>
>
>
> During relion 3D refinement I received the error – please see below.
>
>
>
> Prehistory – I run the Bayesian polishing with the relion 3D refinement
> dataset (syntax error near unexpected token `(').
>
> I suspect there are some errors in Bayesian polishing outcome dataset.
> Some of them I fixed by deleting black images.
>
>
>
> So the question is how to fix the remaining errors to let the relion 3D
> refinement run?
>
>
>
> Thank you in advance,
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
> RUNNING PROTOCOL -----------------
>
> 00002:   Hostname: localhost4.localdomain4
>
> 00003:   PID: 86173
>
> 00004:   pyworkflow: 3.0.16
>
> 00005:   plugin: relion
>
> 00006:   plugin v: 3.1.2
>
> 00007:   currentDir:
> /home/user/Data/ScipionUserData/projects/Colette__03_06__20
>
> 00008:   workingDir: Runs/065340_ProtRelionRefine3D
>
> 00009:   runMode: Continue
>
> 00010:             MPI: 7
>
> 00011:         threads: 6
>
> 00012:   /bin/sh: -c: line 0: syntax error near unexpected token `('
>
> 00013:   /bin/sh: -c: line 0: ` relion_image_handler --i
> Runs/064975_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
> --o
> Runs/065340_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
> --angpix 0.96120 --rescale_angpix 0.96120 --new_box 384 --threshold_above 1
> --threshold_below 0'
>
> 00014:   ** Running command:  relion_image_handler --i
> Runs/064975_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
> --o
> Runs/065340_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
> --angpix 0.96120 --rescale_angpix 0.96120 --new_box 384 --threshold_above 1
> --threshold_below 0
>
> 00015:   Traceback (most recent call last):
>
> 00016:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 197, in run
>
> 00017:       self._run()
>
> 00018:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1361, in _run
>
> 00019:       self._insertAllSteps()  # Define steps for execute later
>
> 00020:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 740, in _insertAllSteps
>
> 00021:       self._insertRelionStep()
>
> 00022:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 751, in _insertRelionStep
>
> 00023:       self._setNormalArgs(args)
>
> 00024:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 969, in _setNormalArgs
>
> 00025:       self._setBasicArgs(args)
>
> 00026:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 1038, in _setBasicArgs
>
> 00027:       self._setMaskArgs(args)
>
> 00028:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_base.py",
> line 1065, in _setMaskArgs
>
> 00029:       mask = relion.convert.convertMask(self.referenceMask.get(),
>
> 00030:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/convert/convert_utils.py",
> line 224, in convertMask
>
> 00031:       pwutils.runJob(None, 'relion_image_handler', params,
> env=Plugin.getEnviron())
>
> 00032:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 52, in runJob
>
> 00033:       return runCommand(command, env, cwd)
>
> 00034:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 67, in runCommand
>
> 00035:       check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr,
>
> 00036:     File
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/subprocess.py",
> line 364, in check_call
>
> 00037:       raise CalledProcessError(retcode, cmd)
>
> 00038:   subprocess.CalledProcessError: Command ' relion_image_handler --i
> Runs/064975_ProtImportMask/extra/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
> --o
> Runs/065340_ProtRelionRefine3D/tmp/cryosparc_P12_J26_008_volume_mask_refine(2).mrc
> --angpix 0.96120 --rescale_angpix 0.96120 --new_box 384 --threshold_above 1
> --threshold_below 0' returned non-zero exit status 1.
>
> 00039:   ------------------- PROTOCOL FAILED (DONE 0/0)
>
>
>
>
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