Re: [scipion-users] relion postprocessing error

[Pablo C. <pc...@cn...>]

Hi Dmitry, probably that (1) in the mask name is causing the error.

Rename it, remove the (), and might work.


On 29/7/21 23:47, Dmitry A. Semchonok wrote:
>
> Dear colleagues,
>
> The issue with relion postprocessing (please see below)
>
> Any suggestions?
>
> Thank you
>
> Sincerely,
>
> Dmitry
>
> 00009:   runMode: Restart
>
> 00010:             MPI: 1
>
> 00011:         threads: 1
>
> 00012:    Starting at step: 1
>
> 00013:    Running steps
>
> 00014:   STARTED: convertInputStep, step 1, time 2021-07-29 
> 23:44:34.952023
>
> 00015:   /bin/sh: -c: line 0: syntax error near unexpected token `('
>
> 00016:   /bin/sh: -c: line 0: ` relion_image_handler --i 
> Runs/009364_ProtImportMask/extra/cryosparc_P17_J22_009_volume_mask_refine(1).mrc 
> --o Runs/009432_ProtRelionPostprocess/input/input_mask.mrc --angpix 
> 0.59200 --rescale_angpix 0.59200 --new_box 320 --threshold_above 1 
> --threshold_below 0'
>
> 00017:   ** Running command:  relion_image_handler --i 
> Runs/009364_ProtImportMask/extra/cryosparc_P17_J22_009_volume_mask_refine(1).mrc 
> --o Runs/009432_ProtRelionPostprocess/input/input_mask.mrc --angpix 
> 0.59200 --rescale_angpix 0.59200 --new_box 320 --threshold_above 1 
> --threshold_below 0
>
> 00018:   Traceback (most recent call last):
>
> 00019:     File 
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 197, in run
>
> 00020:       self._run()
>
> 00021:     File 
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 248, in _run
>
> 00022:       resultFiles = self._runFunc()
>
> 00023:     File 
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 244, in _runFunc
>
> 00024:       return self._func(*self._args)
>
> 00025:     File 
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_postprocess.py", 
> line 199, in convertInputStep
>
> 00026: convert.convertMask(self.solventMask.get(),
>
> 00027:     File 
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/convert/convert_utils.py", 
> line 224, in convertMask
>
> 00028: pwutils.runJob(None, 'relion_image_handler', params, 
> env=Plugin.getEnviron())
>
> 00029:     File 
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", 
> line 52, in runJob
>
> 00030:       return runCommand(command, env, cwd)
>
> 00031:     File 
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", 
> line 67, in runCommand
>
> 00032:   check_call(command, shell=True, stdout=sys.stdout, 
> stderr=sys.stderr,
>
> 00033:     File 
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 
> 364, in check_call
>
> 00034:       raise CalledProcessError(retcode, cmd)
>
> 00035: subprocess.CalledProcessError: Command ' relion_image_handler 
> --i 
> Runs/009364_ProtImportMask/extra/cryosparc_P17_J22_009_volume_mask_refine(1).mrc 
> --o Runs/009432_ProtRelionPostprocess/input/input_mask.mrc --angpix 
> 0.59200 --rescale_angpix 0.59200 --new_box 320 --threshold_above 1 
> --threshold_below 0' returned non-zero exit status 1.
>
> 00036:   Protocol failed: Command ' relion_image_handler --i 
> Runs/009364_ProtImportMask/extra/cryosparc_P17_J22_009_volume_mask_refine(1).mrc 
> --o Runs/009432_ProtRelionPostprocess/input/input_mask.mrc --angpix 
> 0.59200 --rescale_angpix 0.59200 --new_box 320 --threshold_above 1 
> --threshold_below 0' returned non-zero exit status 1.
>
> 00037:   FAILED: convertInputStep, step 1, time 2021-07-29 23:44:35.022128
>
> 00038:   *** Last status is failed
>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*