Re: [scipion-users] Bayesian polishing issue

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Oh, I see. You are probably one of the first users trying to combine
cryosparc and relion protocols in scipion. I will investigate whether
cryosparc plugin does not keep the original micrographName and get back to
you.

Did you run motion correction also in cryosparc or in relion?

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 Tue, Dec 29, 2020 at 2:36 PM Dmitry Semchonok <sem...@gm...>
wrote:

> Dear Grigory,
>
>
>
> Thank you.
>
>
>
> That is quite interesting result.
>
> Could you please check the new Bayesian run (I  copied the files and will
> send you with Wetransfer again)
>
>
>
> If the problem remains the same it means that the cryosparc 3D refine
> output can not be followed up with relion Bayesian polishing.
>
>
>
> Please see the project tree.
>
>
>
>
>
>
>
> What is your opinion?
>
>
>
>
>
>
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
>
>
>
>
>
>
>
>
> Отправлено из приложения "Почта
> <https://go.microsoft.com/fwlink/?LinkId=550986>" для Windows 10
>
>
>
> *От: *Grigory Sharov <sha...@gm...>
> *Отправлено: *29 декабря 2020 г. в 16:22
> *Кому: *Mailing list for Scipion users
> <sci...@li...>
> *Тема: *Re: [scipion-users] Bayesian polishing issue
>
>
>
> Hi,
>
>
>
> Thank you for sending over the files. rlnMicrographName in the
> input_particles.star and input_corrected_micrographs.star are completely
> different. I do not know how you have generated your particles, but you
> cannot run polishing with them.
>
>
>
> rlnMicrographName
>
> 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 Tue, Dec 29, 2020 at 11:32 AM Grigory Sharov <sha...@gm...>
> wrote:
>
> Hi,
>
>
>
> You forgot to attach Runs/004138_ProtRelionBayesianPolishing/input_particles.star
> file
>
>
>
> On Tue, Dec 29, 2020, 11:26 Dmitry Semchonok <sem...@gm...> wrote:
>
> Dear Grigory,
>
>
>
> Please find the file attached
>
>
>
> Thank you!
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
> On Tue, Dec 29, 2020 at 12:28 AM Grigory Sharov <sha...@gm...>
> wrote:
>
> Hi Dmitry,
>
>
>
> this usually happens if you have moved your raw movie files from where
> Scipion expects them to be.
>
>
>
> Could you please send me
> Runs/004138_ProtRelionBayesianPolishing/input_particles.star and
> Runs/004138_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> files?
>
>
> 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, Dec 28, 2020 at 10:16 PM Dmitry Semchonok <sem...@gm...>
> wrote:
>
> Dear colleagues,
>
>
>
> *Bayesian polishing issue –*
>
>
>
>
>
> 00008:   workingDir: Runs/004138_ProtRelionBayesianPolishing
>
> 00009:   runMode: Restart
>
> 00010:             MPI: 1
>
> 00011:         threads: 14
>
> 00012:    Starting at step: 1
>
> 00013:    Running steps
>
> 00014:   STARTED: convertInputStep, step 1, time 2020-12-28 23:03:24.304754
>
> 00015:   Converting set from
> 'Runs/003937_ProtRelionRefine3D/particles.sqlite' into
> 'Runs/004138_ProtRelionBayesianPolishing/input_particles.star'
>
> 00016:   convertBinaryFiles: creating soft links.
>
> 00017:      Root:
> Runs/004138_ProtRelionBayesianPolishing/input/particles/input ->
> Runs/000427_ProtRelionExtractParticles/extra
>
> 00018:   FINISHED: convertInputStep, step 1, time 2020-12-28
> 23:04:33.416996
>
> 00019:   STARTED: trainOrPolishStep, step 2, time 2020-12-28
> 23:04:33.422574
>
> 00020:   relion_motion_refine --i
> Runs/004138_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/004138_ProtRelionBayesianPolishing/extra --f
> Runs/004089_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.59200 --corr_mic
> Runs/004138_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 3 --last_frame 0 --min_p 421029 --eval_frac 0.500
> --align_frac 0.500 --params3 --j 14
>
> 00021:    + Reading
> Runs/004138_ProtRelionBayesianPolishing/input_particles.star..
>
> 00022:   in:
> /home/user/Data/Software/Scipion3/software/em/relion-3.1.0/src/jaz/micrograph_handler.cpp,
> line 261
>
> 00023:   ERROR:
>
> 00024:   There is no movie metadata STAR file for any micrographs!
>
> 00025:   === Backtrace  ===
>
> 00026:   relion_motion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x453571]
>
> 00027:
> relion_motion_refine(_ZN17MicrographHandler11loadInitialERKSt6vectorI13MetaDataTableSaIS1_EEbRiRdRSs+0xb95)
> [0x531275]
>
> 00028:
> relion_motion_refine(_ZN17MicrographHandler4initERKSt6vectorI13MetaDataTableSaIS1_EEbiRiRdRSs+0x78)
> [0x533a88]
>
> 00029:   relion_motion_refine(_ZN13MotionRefiner4initEv+0x546) [0x47d1a6]
>
> 00030:   relion_motion_refine(main+0x31) [0x428841]
>
> 00031:   /lib64/libc.so.6(__libc_start_main+0xf5) [0x7ff26cfb7555]
>
> 00032:   relion_motion_refine() [0x42955f]
>
> 00033:   ==================
>
> 00034:   ERROR:
>
> 00035:   There is no movie metadata STAR file for any micrographs!
>
> 00036:   Traceback (most recent call last):
>
> 00037:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 189, in run
>
> 00038:       self._run()
>
> 00039:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 240, in _run
>
> 00040:       resultFiles = self._runFunc()
>
> 00041:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 236, in _runFunc
>
> 00042:       return self._func(*self._args)
>
> 00043:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py",
> line 309, in trainOrPolishStep
>
> 00044:       self.runJob(prog, args)
>
> 00045:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
> line 1357, in runJob
>
> 00046:       self._stepsExecutor.runJob(self._log, program, arguments,
> **kwargs)
>
> 00047:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
> line 65, in runJob
>
> 00048:       process.runJob(log, programName, params,
>
> 00049:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 51, in runJob
>
> 00050:       return runCommand(command, env, cwd)
>
> 00051:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py",
> line 66, in runCommand
>
> 00052:       check_call(command, shell=True, stdout=sys.stdout,
> stderr=sys.stderr,
>
> 00053:     File
> "/home/user/.conda/envs/.scipion3env/lib/python3.8/subprocess.py", line
> 364, in check_call
>
> 00054:       raise CalledProcessError(retcode, cmd)
>
> 00055:   subprocess.CalledProcessError: Command 'relion_motion_refine --i
> Runs/004138_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/004138_ProtRelionBayesianPolishing/extra --f
> Runs/004089_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.59200 --corr_mic
> Runs/004138_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 3 --last_frame 0 --min_p 421029 --eval_frac 0.500
> --align_frac 0.500 --params3 --j 14 ' returned non-zero exit status 1.
>
> 00056:   Protocol failed: Command 'relion_motion_refine --i
> Runs/004138_ProtRelionBayesianPolishing/input_particles.star --o
> Runs/004138_ProtRelionBayesianPolishing/extra --f
> Runs/004089_ProtRelionPostprocess/extra/postprocess.star --angpix_ref
> 0.59200 --corr_mic
> Runs/004138_ProtRelionBayesianPolishing/input_corrected_micrographs.star
> --first_frame 3 --last_frame 0 --min_p 421029 --eval_frac 0.500
> --align_frac 0.500 --params3 --j 14 ' returned non-zero exit status 1.
>
> 00057:   FAILED: trainOrPolishStep, step 2, time 2020-12-28 23:04:45.953315
>
> 00058:   *** Last status is failed
>
> 00059:   ------------------- PROTOCOL FAILED (DONE 2/2)
>
>
>
>
>
>
>
> Any ideas?
>
> Thank you!
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] Bayesian polishing issue

Image processing framework to integrate EM software packages.

Re: [scipion-users] Bayesian polishing issue