Re: [scipion-users] Bayesian polishing

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

Hi Dmitry,

I think you posted a similar error before. You are using too many particles
for training and running out of RAM, hence your process is killed by Linux
kernel.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Thu, Jun 10, 2021 at 4:02 PM Dmitry Semchonok <Sem...@gm...>
wrote:

> 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
>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>