#!/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

tablein=/data/mramseylab/16S/proc_reads/2022_AL_SUPP/filteredsamples_2022/
metadir=/data/mramseylab/16S/metadata/plaque_meta_3.tsv
treedir=/data/mramseylab/raw_reads/2022_AL_SUPP/AL_2022
visdir=/data/mramseylab/16S/visualizations/AL_2022

module load QIIME2/2024.2

qiime diversity alpha-rarefaction \
  --i-table $tablein/filtered_samples.qza \
  --i-phylogeny $treedir/rooted-tree-1.qza \
  --p-max-depth 10000 \
  --m-metadata-file $metadir \
  --o-visualization $visdir/alpha-rarefaction-10000-2022.qzv