Re: [scipion-users] Bayesian polishing

[Pablo C. <pc...@cn...>]

Hi Dmitry, I've seen this then there is a movie with less frames than 
the rest. Sets of movies are meant to be homogeneous in terms of number 
of frames, but if a movie file is "partially corrupted" (I've seen tiff 
files partially donwloaded that motioncor is able to process) then that 
movie slips into the set and makes bayesian polishing fails.

What can you do?

1.- Identify the corrupted movies: Probably their size will be smaller 
the the others.

2.- Make a subset of the movies, removing the corrupted movies

3.- Do the same for the set of particles


On out side, since this has happened several times, we can try to:

A:) avoid corrupted movies to slip in the sets.

B:) tolerate this error in the bayesian polishing protocol and skip this 
case.



On 2/9/21 21:36, Dmitry Semchonok wrote:
>
> Dear colleagues,
>
> The issue with Bayesian polishing –
>
> Logging configured. STDOUT --> 
> Runs/003279_ProtRelionBayesianPolishing/logs/run.stdout , STDERR --> 
> Runs/003279_ProtRelionBayesianPolishing/logs/run.stderr
>
> [32mRUNNING PROTOCOL -----------------[0m
>
> Protocol starts
>
> Hostname: localhost4.localdomain4
>
> PID: 240224
>
> pyworkflow: 3.0.17
>
> plugin: relion
>
> plugin v: 3.1.3
>
> currentDir: /home/user/Data/ScipionUserData/projects/Quentin__august__PSI
>
> workingDir: Runs/003279_ProtRelionBayesianPolishing
>
> runMode: Continue
>
> MPI: 1
>
> threads: 1
>
> Starting at step: 1
>
> Running steps
>
> [35mSTARTED[0m: convertInputStep, step 1, time 2021-09-02 21:31:33.074480
>
> Converting set from 
> 'Runs/002848_ProtCryoSparcNonUniformRefine3D/particles.sqlite' into 
> 'Runs/003279_ProtRelionBayesianPolishing/input_particles.star'
>
> [31mProtocol failed: list index out of range[0m
>
> [35mFAILED[0m: convertInputStep, step 1, time 2021-09-02 21:31:33.532782
>
> *** Last status is failed
>
> [32m------------------- PROTOCOL FAILED (DONE 1/2)[0m
>
> Traceback (most recent call last):
>
>   File 
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 201, in run
>
>     self._run()
>
>   File 
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 252, in _run
>
>     resultFiles = self._runFunc()
>
>   File 
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 248, in _runFunc
>
>     return self._func(*self._args)
>
>   File 
> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_bayesian_polishing.py", 
> line 296, in convertInputStep
>
> tableShifts.addRow(i, shiftsX[i-a0] + xoff,
>
> IndexError: list index out of range
>
> [31mProtocol failed: list index out of range[0m
>
> Any idea?
>
> Thank you
>
> Sincerely,
>
> Dmitry
>
> P.s. also strange behavior of adding movies to the project – the 
> process just hangs without finishing.
>
> Could those 2 issues be connected?
>
> Could that happened after the SCIPION3 updates?
>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*