Re: [scipion-users] Bayesian polishing issue

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

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
>>>
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