#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=2 --ntasks-per-node=2
#SBATCH --mem=48g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2019.7
rawdir=/data/mramseylab/raw_reads/2023_SUPP_V1V2
visdir=/data/mramseylab/visualizations/AL_2023
metadata=/data/mramseylab/metadata/plaque_meta_5.tsv

qiime feature-table summarize \
  --i-table $rawdir/denoise-table-v1v2.qza \
  --o-visualization $visdir/master-table-sum-v1v2.qzv \
  --m-sample-metadata-file $metadata \

qiime feature-table tabulate-seqs \
  --i-data $rawdir/rep-seqs-v1v2.qza \
  --o-visualization $visdir/rep-seqs-v1v2.qzv

qiime phylogeny align-to-tree-mafft-fasttree \
  --i-sequences $rawdir/rep-seqs-v1v2.qza \
  --o-alignment $rawdir/aligned-master-rep-seqs-v1v2.qza \
  --o-masked-alignment $rawdir/masked-aligned-master-rep-seqs-v1v2.qza \
  --o-tree $rawdir/unrooted-tree-master-v1v2.qza \
  --o-rooted-tree $rawdir/rooted-tree-master-v1v2.qza