Re: [scipion-users] Relion -- motion cor error

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

Hi Dmitry,

looking at the time - 1 s - this seems very quick! You need to check the
output in the Runs/000980_ProtRelionMotioncor/tmp/movie_000001/output/
folder if it actually run anything.

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, Nov 24, 2020 at 12:00 PM Dmitry Semchonok <Sem...@gm...>
wrote:

> Dear colleagues,
>
>
> Could you please advice?
>
>
>
> Scipon2 — relion - motion correction — Error
>
> At the same time the motion cor2 runs fine.
>
> Thank you
>
> 0001:   RUNNING PROTOCOL -----------------
> 00002:        HostName: cryoem02
> 00003:             PID: 64478
> 00004:         Scipion: v2.0 (2019-04-23) Diocletian
> 00005:      currentDir:
> /data/panos/ScipionUserData/projects/TutorialBetagel__students
> 00006:      workingDir: Runs/000980_ProtRelionMotioncor
> 00007:         runMode: Continue
> 00008:             MPI: 1
> 00009:         threads: 1
> 00010:   len(steps) 17 len(prevSteps) 0
> 00011:    Starting at step: 1
> 00012:    Running steps
> 00013:   STARTED: _convertInputStep, step 1
> 00014:     2020-11-24 12:56:04.911042
> 00015:   Relion version:
> 00016:   relion_run_motioncorr --version
> 00017:   RELION version: 3.0.8
> 00018:   Precision: BASE=double, CUDA-ACC=single
> 00019:
> 00020:   FINISHED: _convertInputStep, step 1
> 00021:     2020-11-24 12:56:04.951805
> 00022:   STARTED: processMovieStep, step 2
> 00023:     2020-11-24 12:56:04.992562
> 00024:   Processing movie:
> Runs/000980_ProtRelionMotioncor/tmp/movie_000001/Falcon_2012_06_12-14_33_35_0_movie.mrcs
> 00025:   relion_run_motioncorr --i
> Falcon_2012_06_12-14_33_35_0_movie_input.star --o output/ --use_own
> --first_frame_sum 1 --last_frame_sum 16 --bin_factor 1.000000 --bfactor 150
> --angpix 3.540000 --patch_x 1 --patch_y 1 --j 1 --voltage 300
> 00026:    Using our own implementation based on MOTIONCOR2 algorithm
> 00027:    to correct beam-induced motion for the following micrographs:
> 00028:     * Falcon_2012_06_12-14_33_35_0_movie.mrcs
> 00029:    Correcting beam-induced motions using our own implementation ...
> 00030:      1/   1 sec
> ............................................................~~(,_,">
> 00031:    Generating logfile.pdf ...
> 00032:   000/??? sec ~~(,_,">
>              [oo]gs: /usr/local/scipion/v2.0.0/software/lib/libtiff.so.5:
> no version information available (required by /lib64/libgs.so.9)
> 00033:      1/   1 sec
> ............................................................~~(,_,">
> 00034:    Done! Written: output/logfile.pdf and
> output/corrected_micrographs.star
> 00035:   Traceback (most recent call last):
> 00036:     File
> "/usr/local/scipion/v2.0.0/pyworkflow/protocol/protocol.py", line 186, in
> run
> 00037:       self._run()
> 00038:     File
> "/usr/local/scipion/v2.0.0/pyworkflow/protocol/protocol.py", line 237, in
> _run
> 00039:       resultFiles = self._runFunc()
> 00040:     File
> "/usr/local/scipion/v2.0.0/pyworkflow/protocol/protocol.py", line 233, in
> _runFunc
> 00041:       return self._func(*self._args)
> 00042:     File
> "/usr/local/scipion/v2.0.0/pyworkflow/em/protocol/protocol_movies.py", line
> 375, in processMovieStep
> 00043:       self._processMovie(movie)
> 00044:     File
> "/usr/local/scipion/v2.0.0/software/lib/python2.7/site-packages/relion/protocols/protocol_motioncor.py",
> line 213, in _processMovie
> 00045:       self._computeExtra(movie)
> 00046:     File
> "/usr/local/scipion/v2.0.0/software/lib/python2.7/site-packages/relion/protocols/protocol_motioncor.py",
> line 355, in _computeExtra
> 00047:       self._saveAlignmentPlots(movie)
> 00048:     File
> "/usr/local/scipion/v2.0.0/software/lib/python2.7/site-packages/relion/protocols/protocol_motioncor.py",
> line 401, in _saveAlignmentPlots
> 00049:       shiftsX, shiftsY = self._getMovieShifts(movie,
> self._getMovieOutFn(movie, '.star'))
> 00050:     File
> "/usr/local/scipion/v2.0.0/software/lib/python2.7/site-packages/relion/protocols/protocol_motioncor.py",
> line 271, in _getMovieShifts
> 00051:       table = md.Table(fileName=outStar, tableName='global_shift')
> 00052:     File
> "/usr/local/scipion/v2.0.0/software/lib/python2.7/site-packages/relion/convert/metadata.py",
> line 58, in __init__
> 00053:       self.read(fileName, tableName)
> 00054:     File
> "/usr/local/scipion/v2.0.0/software/lib/python2.7/site-packages/relion/convert/metadata.py",
> line 109, in read
> 00055:       with open(fileName) as f:
> 00056:   IOError: [Errno 2] No such file or directory:
> 'Runs/000980_ProtRelionMotioncor/tmp/movie_000001/output/Falcon_2012_06_12-14_33_35_0_movie.star'
> 00057:   Protocol failed: [Errno 2] No such file or directory:
> 'Runs/000980_ProtRelionMotioncor/tmp/movie_000001/output/Falcon_2012_06_12-14_33_35_0_movie.star'
> 00058:   FAILED: processMovieStep, step 2
> 00059:     2020-11-24 12:56:07.086919
> 00060:   *** Last status is failed
> 00061:   ------------------- PROTOCOL FAILED (DONE 2/17)
>
>
> Sincerely
> Dmitry
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