#!/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=/master-denoise-table-v1v2-paired.qza
treein=/rooted-tree-master-v1v2-paired.qza
metadir=/data/mramseylab/metadata/plaque_meta_6.tsv
rawdir=/data/mramseylab/raw_reads/2023_SUPP_V1V2

module load QIIME2/2019.7

qiime diversity alpha-rarefaction \
  --i-table $rawdir$tablein \
  --i-phylogeny $rawdir$treein \
  --p-max-depth 26000 \
  --m-metadata-file $metadir \
  --o-visualization $rawdir/alpha-rarefaction.qzv