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npy2cov.job
39 lines (34 loc) · 1.01 KB
/
npy2cov.job
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#!/bin/bash
#PBS -l select=1:ncpus=1
#PBS -l walltime=5000:00:00
#PBS -N npycov
#PBS -j oe
#PBS -m ae
#PBS -M kprovost@amnh.org
#PBS -k oe
# change to the working directory
cd $PBS_O_WORKDIR
echo "pbsworkdir"
echo $PBS_O_WORKDIR
EXECDIR=`pwd`
export PATH=./:$PATH
echo $PATH
#Arguments:
## GL = genotype likehood file (Beagle format)
cd "/vz-nas1-active/ProcessedGenomicReads/EVERY_PLATE/ANGSD/BEAGLE/"
source activate py36
# for npyfile in /vz-nas1-active/ProcessedGenomicReads/EVERY_PLATE/ANGSD/BEAGLE/*/*/*cov.npy; do
# echo $npyfile
# python /home/kprovost/nas3/ANGSD_pipeline/npy2cov.py $npyfile
# gzip -f $npyfile
# done
# for npyfile in /vz-nas1-active/ProcessedGenomicReads/EVERY_PLATE/ANGSD/BEAGLE/*/*/*/*cov.npy; do
# echo $npyfile
# python /home/kprovost/nas3/ANGSD_pipeline/npy2cov.py $npyfile
# gzip -f $npyfile
# done
for npyfile in /vz-nas1-active/ProcessedGenomicReads/EVERY_PLATE/ANGSD/BEAGLE/*/*/*/*/*cov.npy; do
echo $npyfile;
#python /home/kprovost/nas3/ANGSD_pipeline/npy2cov.py $npyfile;
#gzip -f $npyfile;
done