2.1_LDSR_scores_wave1.sb

#!/bin/bash --login
########## SBATCH Lines for Resource Request ##########
 
#SBATCH --time=4:00:00             # limit of wall clock time - how long the job will run (same as -t)
#SBATCH --nodes=1-48                 # number of different nodes - could be an exact number or a range of nodes (same as -N)
#SBATCH --ntasks=48                # number of tasks - how many tasks (nodes) that you require (same as -n)
#SBATCH --cpus-per-task=2           # number of CPUs (or cores) per task (same as -c)
#SBATCH --mem-per-cpu=64G            # memory required per allocated CPU (or core) - amount of memory (in bytes)
#SBATCH --job-name Wave1      # you can give your job a name for easier identification (same as -J)
 
########## Command Lines to Run ##########
 
module purge

#module load GCC/6.4.0-2.28 OpenMPI  ### load necessary modules, e.g.


#### NOTES ####
## This LDSR program is ridiculously finicky. You can't have any modules loaded, or anything in your path 
## it doesn't expect. I also had to uninstall linuxbrew completely, because for some reason it was 
## still trying to use the linuxbrew glibc *even though it was absolutly not in my path anymore* I 
## don't even know how that's possible.
#######################


#screen 

#qsub -I -N MyJobName -l nodes=1:ppn=24,mem=64gb,walltime=47:00:00

cd $SLURM_SUBMIT_DIR || exit 

export PATH=$PATH:$PWD/tools/bin/

module load Anaconda2/4.2.0


#conda create --name ldsr python=2
source activate ldsr
# pip install pandas==0.17.0 numpy==1.8.0 scipy==0.11.0 bitarray==0.8.3




# ========= ld score estimation =========

# create annot files 
bash src/s6-create-annot.sh s3/subset. *_annots/*_LDSR.txt -f

# create ldscore files based on annots (takes 24h at 8x parallel)
bash src/s7-create-ldscores.sh -j 24 -f


scontrol show job $SLURM_JOB_ID