#!/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/raw_reads/2023_AL_SUPP/triplicates/tripA
metadir=/data/mramseylab/16S/metadata/plaque_meta_A.tsv
visdir=/data/mramseylab/16S/visualizations/AL_2023

module load QIIME2/2024.2

qiime diversity alpha-rarefaction \
  --i-table $tablein/A-saliva-table.qza \
  --i-phylogeny $tablein/rooted-tree-pseudo-A.qza \
  --p-max-depth 1500 \
  --m-metadata-file $metadir \
  --o-visualization $visdir/alpha-rarefaction-subject-A-1500-2023.qzv