-
Notifications
You must be signed in to change notification settings - Fork 0
/
motioncorr_slurm.sh
executable file
·33 lines (25 loc) · 1.71 KB
/
motioncorr_slurm.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
#!/bin/bash
#SBATCH --job-name=mc_stacker
#SBATCH --ntasks={MPIs}
#SBATCH --cpus-per-task={threads}
#SBATCH --output={position_directory}/mc_stacker_{position_prefix}_out.txt
#SBATCH --error={position_directory}/mc_stacker_{position_prefix}_err.txt
#SBATCH --open-mode=append
#SBATCH --partition={partition}
#SBATCH --mem-per-cpu=7G
##SBATCH --exclusive #sometimes solves a bug with imod on the strubi cluster. Turned off by default.
# Print the exact command into the output file for debugging and to log the
# exact RELION version
module purge
module load {relion_module}
echo "------------------------------------------------------------------------------------"
mkdir {position_directory}/Import
mkdir {position_directory}/Import/job001
cd {position_directory}
relion_import --do_movies --optics_group_name "opticsGroup1" --angpix {pixel_size} --kV {voltage} --Cs {Cs} --Q0 {Q0} --beamtilt_x 0 --beamtilt_y 0 --i "*.{file_type}" --odir Import/job001/ --ofile movies.star --pipeline_control Import/job001/
mpirun -n {MPIs} $(which relion_run_motioncorr_mpi) --i Import/job001/movies.star --o MotionCorr/job002/ --first_frame_sum 1 --last_frame_sum -1 --use_own --j {threads} --bin_factor 1 --bfactor 150 --dose_per_frame {frame_dose} --preexposure 0 --patch_x {motioncorr_patches} --patch_y {motioncorr_patches} --eer_grouping {eer_grouping} --dose_weighting --only_do_unfinished --pipeline_control MotionCorr/job002/ --save_noDW true --gainref {gainref}
module purge
module load {imod_module}
newstack -fileinlist {position_prefix}_newstack.txt -output {position_prefix}_unaligned.mrc
#ccderaser {position_prefix}.st {position_prefix}.st -find
echo "------------------------------------------------------------------------------------"