Re: [scipion-users] Bayesian polishing issue

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

Hi,

please check:

1) _rlnMicrographName in input_particles.star and
input_corrected_micrographs.star
match
2) you have _rlnMicrographMetadata star files that contain correct
information

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 Mon, Jul 26, 2021 at 8:56 PM Dmitry A. Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
>
>
> Issue with Bayesian polishing.
>
>
>
> The error says that the metadata was not found, my understanding is that
> original files are not on the place but currently this is not the case.
>
> Would you please prompt what can case the issue?
>
>
>
> Thank you!
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
> Hostname: cryoem01
>
> PID: 37775
>
> pyworkflow: 3.0.16
>
> plugin: relion
>
> plugin v: 3.1.2
>
> currentDir: /data1/ScipionUserData/projects/20201211_apof_ph5_pos4
>
> workingDir: Runs/009050_ProtRelionBayesianPolishing
>
> runMode: Continue
>
>           MPI: 1
>
>       threads: 1
>
> Starting at step: 1
>
> Running steps
>
> [35mSTARTED[0m: convertInputStep, step 1, time 2021-07-26 21:49:10.454974
>
> Converting set from
> 'Runs/008377_ProtCryoSparcNewNonUniformRefine3D/particles.sqlite' into
> 'Runs/009050_ProtRelionBayesianPolishing/input_particles.star'
>
> convertBinaryFiles: creating soft links.
>
>    Root: Runs/009050_ProtRelionBayesianPolishing/input/particles/input ->
> Runs/000427_ProtRelionExtractParticles/extra
>
> [35mFINISHED[0m: convertInputStep, step 1, time 2021-07-26 21:49:56.565214
>
> [35mSTARTED[0m: trainOrPolishStep, step 2, time 2021-07-26 21:49:56.684070
>
> [32m relion_motion_refine --i
> Runs/009050_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/009050_ProtRelionBayesianPolishing/extra --f
> Runs/008533_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.59200 --corr_mic
> Runs/009050_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 1 --last_frame 0 --min_p 10000 --eval_frac 0.500 --align_frac
> 0.500 --params3 --j 1 [0m
>
> + Reading Runs/009050_ProtRelionBayesianPolishing/input_particles.star...
>
> in: /opt/Scipion3/software/em/relion-3.1.2/src/jaz/micrograph_handler.cpp,
> line 264
>
> ERROR:
>
> There is no movie metadata STAR file for any micrographs!
>
> === Backtrace  ===
>
> relion_motion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x47e9d1]
>
> relion_motion_refine(_ZN17MicrographHandler11loadInitialERKSt6vectorI13MetaDataTableSaIS1_EEbRiRdRSs+0xa60)
> [0x582890]
>
> relion_motion_refine(_ZN17MicrographHandler4initERKSt6vectorI13MetaDataTableSaIS1_EEbiRiRdRSs+0x78)
> [0x585fc8]
>
> relion_motion_refine(_ZN13MotionRefiner4initEv+0x516) [0x5077d6]
>
> relion_motion_refine(main+0x31) [0x440391]
>
> /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f653431f555]
>
> relion_motion_refine() [0x444570]
>
> ==================
>
> ERROR:
>
> There is no movie metadata STAR file for any micrographs!
>
> Traceback (most recent call last):
>
>   File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 197, in run
>
>     self._run()
>
>   File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 248, in _run
>
>     resultFiles = self._runFunc()
>
>   File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 244, in _runFunc
>
>     return self._func(*self._args)
>
>   File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py",
> line 351, in trainOrPolishStep
>
>     self.runJob(self._getProgram('relion_motion_refine'), args)
>
>   File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1389, in runJob
>
>     self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
>
>   File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
> line 65, in runJob
>
>     process.runJob(log, programName, params,
>
>   File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 52, in runJob
>
>     return runCommand(command, env, cwd)
>
>   File
> "/usr/local/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 67, in runCommand
>
>     check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
>
>   File "/usr/local/miniconda/envs/scipion3/lib/python3.8/subprocess.py",
> line 364, in check_call
>
>     raise CalledProcessError(retcode, cmd)
>
> subprocess.CalledProcessError: Command ' relion_motion_refine --i
> Runs/009050_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/009050_ProtRelionBayesianPolishing/extra --f
> Runs/008533_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.59200 --corr_mic
> Runs/009050_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 1 --last_frame 0 --min_p 10000 --eval_frac 0.500 --align_frac
> 0.500 --params3 --j 1 ' returned non-zero exit status 1.
>
> [31mProtocol failed: Command ' relion_motion_refine --i
> Runs/009050_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/009050_ProtRelionBayesianPolishing/extra --f
> Runs/008533_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.59200 --corr_mic
> Runs/009050_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 1 --last_frame 0 --min_p 10000 --eval_frac 0.500 --align_frac
> 0.500 --params3 --j 1 ' returned non-zero exit status 1.[0m
>
> [35mFAILED[0m: trainOrPolishStep, step 2, time 2021-07-26 21:50:07.277034
>
> *** Last status is failed
>
> [32m------------------- PROTOCOL FAILED (DONE 2/2)[0m
>
>
>
>
>
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>
>
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