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

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

Hello Roman,

most likely you are running out of RAM (process killed by Linux OOM).
Motioncorr process needs at least frame width ∗ height ∗ (frames + 2 +
threads per mpi) ∗ 4 bytes of RAM. Try to increase the number of threads if
possible.

PS. Your dose per frame is wrong (cannot be 45), but that is not related to
the error.


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 Wed, Jun 21, 2023 at 8:23 AM Pablo Conesa <pc...@cn...> wrote:

> 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
>
>
> _______________________________________________
> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
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