#!/bin/bash -l
  
#SBATCH --partition=cpu-standard
#SBATCH --job-name=qualityfilter2
#SBATCH --output=quality_filter2.out
#SBATCH --error=quality_filter2.err
#SBATCH --nodes=1
#SBATCH --mem=64G
#SBATCH --ntasks=4
#SBATCH --qos=short
 
export HOME=/scratch/${USER}
export TMPDIR=/scratch/${USER}/tmp/${SLURM_JOB_ID}
mkdir -p $TMPDIR

module load qiime/qiime2-2019.10 
source activate $QIIME_PATH
  
qiime quality-filter q-score-joined \
  --i-demux demux-joined.qza \
  --p-min-quality 20 \ 
  --o-filtered-sequences demux_joined_filtered2.qza \
  --o-filter-stats demux_joined_filter_stats2.qza