[scipion-users] Bayesian polishing

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

Dear colleagues,

After running Bayesian polishing script with 5e I got the following error



2232: GridSquare_26409500_Data_FoilHole_26633166_Data_26416121_26416123_20210330_110202_Fractions.mrc
02591:           1914: GridSquare_26409382_Data_FoilHole_26635345_Data_26416121_26416123_20210330_172633_Fractions.mrc
02592:           1985: GridSquare_26409382_Data_FoilHole_26635480_Data_26416121_26416123_20210330_201730_Fractions.mrc
02593:           2253: GridSquare_26409500_Data_FoilHole_26633222_Data_26416121_26416123_20210330_123213_Fractions.mrc
02594:           1404: GridSquare_26409268_Data_FoilHole_26621354_Data_26416121_26416123_20210329_092746_Fractions.mrc
02595:           361: GridSquare_26409080_Data_FoilHole_26614677_Data_26416121_26416123_20210328_095659_Fractions.mrc
02596:   
02597:      - Warning: this dataset does not contain 217187 particles (--min_p) in micrographs with at least 2 particles
02598:    + preparing alignment data... 
02599:   Traceback (most recent call last):
02600:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run
02601:       self._run()
02602:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run
02603:       resultFiles = self._runFunc()
02604:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc
02605:       return self._func(*self._args)
02606:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", line 351, in trainOrPolishStep
02607:       self.runJob(self._getProgram('relion_motion_refine'), args)
02608:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1388, in runJob
02609:       self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
02610:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob
02611:       process.runJob(log, programName, params,
02612:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob
02613:       return runCommand(command, env, cwd)
02614:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand
02615:       check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
02616:     File "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
02617:       raise CalledProcessError(retcode, cmd)
02618:   subprocess.CalledProcessError: Command ' relion_motion_refine --i Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o Runs/004833_ProtRelionBayesianPolishing/extra --f Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.
02619:   Protocol failed: Command ' relion_motion_refine --i Runs/004833_ProtRelionBayesianPolishing/input_particles.star --o Runs/004833_ProtRelionBayesianPolishing/extra --f Runs/004384_ProtRelionPostprocess/extra/postprocess.star --angpix_ref 0.59200 --corr_mic Runs/004833_ProtRelionBayesianPolishing/input_corrected_micrographs.star --first_frame 1 --last_frame 10 --min_p 217187 --eval_frac 0.500 --align_frac 0.500 --params3 --j 14 ' died with <Signals.SIGKILL: 9>.
02620:   FAILED: trainOrPolishStep, step 2, time 2021-06-09 11:27:00.176491
02621:   *** Last status is failed 
02622:   ------------------- PROTOCOL FAILED (DONE 2/2)

Do you know how to fix that?


Thank you

Sincerely,
Dmitry