Re: [scipion-users] Bayesian polishing issue

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

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
>