Re: [scipion-users] Bayesian polishing issue

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

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
>>>>
>>>>
>>>>
>>>>
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>>>>
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