Re: [scipion-users] SCIPON 2--> SCIPION 3.0 relion-motioncor

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

Hi Dmitry,

could you please send me:

- Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star
,
- first hundred lines of
Runs/037414_ProtRelionBayesianPolishing/input_particles.star and
- any star file from Runs/037414_ProtRelionBayesianPolishing/input/ folder?

then we can go from there.

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, Nov 30, 2020 at 3:13 PM Dmitry Semchonok <Sem...@gm...>
wrote:

> Dear colleagues,
>
>
>
> A compatibility question:
>
>
>
> I have a project done by SCIPION 2.0: including relion particle polishing
>
>  Now when I open it with SCIPION 3.0 all works fine except Bayesian
> polishing.
>
>
> The error is :
>
> Using dose per frame from
> Runs/037414_ProtRelionBayesianPolishing/input/FoilHole_15002836_Data_15054168_15054170_20200615_191823_Fractions.star:
> 1 e/A^2
>
> 02673:   in:
> /home/user/Data/Software/Scipion3/software/em/relion-3.1.0/src/jaz/micrograph_handler.cpp,
> line 211
>
> 02674:   ERROR:
>
> 02675:   ERROR: Not a single movie contains the requested number of frames
> (119)
>
> 02676:   === Backtrace  ===
>
> 02677:   relion_motion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x453571]
>
> 02678:
> relion_motion_refine(_ZN17MicrographHandler20findLongEnoughMoviesERKSt6vectorI13MetaDataTableSaIS1_EEii+0x44d)
> [0x53272d]
>
> 02679:   relion_motion_refine(_ZN13MotionRefiner4initEv+0xee3) [0x47db43]
>
> 02680:   relion_motion_refine(main+0x31) [0x428841]
>
> 02681:   /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fd0b7c19555]
>
> 02682:   relion_motion_refine() [0x42955f]
>
> 02683:   ==================
>
> 02684:   ERROR:
>
> 02685:   ERROR: Not a single movie contains the requested number of frames
> (119)
>
> 02686:   Traceback (most recent call last):
>
> 02687:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 187, in run
>
> 02688:       self._run()
>
> 02689:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 238, in _run
>
> 02690:       resultFiles = self._runFunc()
>
> 02691:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 234, in _runFunc
>
> 02692:       return self._func(*self._args)
>
> 02693:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py",
> line 309, in trainOrPolishStep
>
> 02694:       self.runJob(prog, args)
>
> 02695:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1338, in runJob
>
> 02696:       self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)
>
> 02697:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
> line 65, in runJob
>
> 02698:       process.runJob(log, programName, params,
>
> 02699:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 51, in runJob
>
> 02700:       return runCommand(command, env, cwd)
>
> 02701:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 66, in runCommand
>
> 02702:       check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr,
>
> 02703:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/subprocess.py", line
> 364, in check_call
>
> 02704:       raise CalledProcessError(retcode, cmd)
>
> 02705:   subprocess.CalledProcessError: Command 'relion_motion_refine --i
> Runs/037414_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/037414_ProtRelionBayesianPolishing/extra --f
> Runs/037365_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.96120 --corr_mic
> Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 2 --last_frame 0 --min_p 49704 --eval_frac 0.500 --align_frac
> 0.500 --params3 --j 14 ' returned non-zero exit status 1.
>
> 02706:   Protocol failed: Command 'relion_motion_refine --i
> Runs/037414_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/037414_ProtRelionBayesianPolishing/extra --f
> Runs/037365_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.96120 --corr_mic
> Runs/037414_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 2 --last_frame 0 --min_p 49704 --eval_frac 0.500 --align_frac
> 0.500 --params3 --j 14 ' returned non-zero exit status 1.
>
> 02707:   FAILED: trainOrPolishStep, step 2, time 2020-11-30 16:07:27.531346
>
> 02708:   *** Last status is failed
>
> 02709:   ------------------- PROTOCOL FAILED (DONE 2/2)
>
>
>
>
>
> Could that be a consequence that the motion correction was done in
> relion-motioncor protocol in SCIPION 2.0 and SCIPION 3.0 has the newer
> relion-motion correction protocol? (The indirect sign I see in the output
> relion-motioncor file).
>
>
>
> Thank you in advance.
>
>
>
> Sincerely,
>
> Dmitry
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