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

[ROMAN A. <romanaguirre@g.ucla.edu>]

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