[scipion-users] Relion -- motion cor error

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

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