#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=24g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL


module load QIIME2/2024.2

tabledir=/data/mramseylab/16S/proc_reads/2024_AL_SUPP_6000/FST0
clsdir=/data/mramseylab/16S/classifiers/homd-classifier/taxonomy.qza
visdir=/data/mramseylab/16S/visualizations/AL_2024/FST0-filtered
metadir=/data/mramseylab/16S/metadata/meta_BSFS.tsv

qiime taxa collapse \
  --i-table $tabledir/filtered-reads.qza \
  --i-taxonomy $clsdir \
  --p-level 6 \
  --o-collapsed-table $tabledir/FST0-table-lvl6.qza