Re: [scipion-users] relion postprocessing error

[Dmitry S. <Sem...@gm...>]

Dear Pablo,

Thanks - indeed I tried that yesterday and everything worked out.

Sincerely,
Dmitry



> On 30. Jul 2021, at 09:03, Pablo Conesa <pc...@cn...> wrote:
> 
> 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
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