#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=144g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2024.2

qiime feature-classifier extract-reads \
    --i-sequences silva-138.1-ssu-c97-seqs-derep-lca.qza \
    --p-f-primer AGAGTTTGATYMTGGCTCAG \
    --p-r-primer TGCTGCCTCCCGTAGRAGT \
    --p-n-jobs 2 \
    --p-read-orientation 'forward' \
    --o-reads silva-138.1-ssu-nr99-seqs-29f-338r.qza