#!/bin/bash
## modified by Yixiao by 02/07/2017
## specify queue
#SBATCH -p hpc,cem_lenovo
## run time
#SBATCH -t 202:00:00
## number of nodes, this was on stampede, may not need this at your site
#SBATCH -N 5
## number of threads
##SBATCH  --cpus-per-task=1
## number of cores
#SBATCH -n 120 
## error and output files, %J is a handy variable.
#SBATCH --error=Extract/job150/run.err
#SBATCH --output=Extract/job150/run.out

## Job Name
#SBATCH -J Extract/job150/
## email when it is done
#SBATCH --mail-type=end
#SBATCH --mail-user=scai@rockefeller.edu

mpirun --map-by node -n 120  `which relion_preprocess_mpi` --i CtfFind/job147/micrographs_ctf.star --coord_dir Import/job149/ --coord_suffix _automatch.star --part_star Extract/job150/particles.star --part_dir Extract/job150/ --extract --extract_size 200 --scale 100 --norm --bg_radius 37 --white_dust -1 --black_dust -1 --invert_contrast