Re: [scipion-users] Scipion installation and using Relion's MOTIONCOR2

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

Hi Roman, could you please post the full run.stderr?

On 21/6/23 1:34, ROMAN AGUIRRE wrote:
> Hello all,
> I was recently at the data processing workshop at SLAC, and wanted to 
> try using Scipion on some of my data after seeing what its capable of. 
> I installed it on a WSL workstation, and starting Scipion and 
> installing plugins so far has not resulted in any errors. However, I 
> ran into problems right away when trying to use Relion's motioncor2. 
> Although it does say that the job is running, the output logs show the 
> following errors:
>
> on run.stdout, it shows
>
> 00207:    relion_run_motioncorr --i PDC__00021_input.star --o output/ 
> --use_own --first_frame_sum 1 --last_frame_sum 40 --bin_factor 
> 1.000000 --bfactor 150 --angpix 1.36000 --patch_x 5 --patch_y 5 
> --group_frames 1 --j 7 --gainref 
> "/home/romana/Documents/gain_reference_7676x7420_190815s.mrc" 
> --gain_rot 0 --gain_flip 0 --grouping_for_ps 1 --dose_weighting 
> --dose_per_frame 45.000000 --preexposure 0.000000
> 00208:    Using our own implementation based on MOTIONCOR2 algorithm
> 00209:    to correct beam-induced motion for the following micrographs:
> 00210:     * PDC__00021.tif
> 00211:    Correcting beam-induced motions using our own implementation ...
> 00212:   000/??? sec ~~(,_,">                           
>  [oo]Erasing.....movieFolder: 
> Runs/000118_ProtRelionMotioncor/tmp/movie_000016
> 00213:   FINISHED: processMovieStep, step 17, time 2023-06-20 
> 16:16:05.085374
> 00214:   ERROR: Movie 
> Runs/000002_ProtImportMovies/extra/PDC__00021.tif couldn't be added to 
> the output set.
> 00215:   [Errno 2] No such file or directory: 
> 'Runs/000118_ProtRelionMotioncor/extra/PDC__00021.star'
> 00216:   WARNING: Micrograph 
> Runs/000118_ProtRelionMotioncor/extra/PDC__00021_aligned_mic_DW.mrc 
> was not generated, can't add it to output set.
>
> and on run.stderr
>
> 00033:   Killed
> 00034:   ERROR processing movie: PDC__00022.tif
>
> I was wondering what steps I could take to fix this. I have tried 
> uninstalling and re-installing the relion plugin, as well as checking 
> that all the proper dependencies are installed on my workstation. 
> However, I have been unable to pinpoint what is specifically causing 
> the error. If this is not the right place to ask for this type of 
> help, please let me know. Thank you for your time.
>
> Sincerely,
> Roman Aguirre
>
> Roman Aguirre
> PhD Student | Zhou Lab
> UCLA | Chemistry and Biochemistry
> romanaguirre@g.ucla.edu
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*