#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=2 --ntasks-per-node=1
#SBATCH --mem=64g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2019.7
array=( An )

for i in "${array[@]}"
do

rawdir=/data/mramseylab/raw_reads/trip"$i"
visdir=/data/mramseylab/scripts/ALScripts/triptest/visualizations_"$i"
metadata=/data/mramseylab/metadata/plaque_meta_"$i".tsv


  qiime dada2 denoise-paired \
    --i-demultiplexed-seqs $rawdir/demux-master-pseudo-"$i".qza \
    --p-trim-left-f 6 \
    --p-trim-left-r 6 \
    --p-trunc-len-f 288 \
    --p-trunc-len-r 204 \
    --o-table $rawdir/paired-pseudo-denoise-table-"$i".qza \
    --o-representative-sequences $rawdir/paired-pseudo-reps-seq-"$i".qza \
    --o-denoising-stats $rawdir/denoise-pseudo-paired-"$i".qza


qiime feature-table summarize \
  --i-table $rawdir/paired-pseudo-denoise-table-"$i".qza \
  --o-visualization $visdir/denoise-table-"$i".qzv \
  --m-sample-metadata-file $metadata \

qiime feature-table tabulate-seqs \
  --i-data $rawdir/paired-pseudo-reps-seq-"$i".qza \
  --o-visualization $visdir/denoise-pseudo-paired-"$i".qzv

qiime phylogeny align-to-tree-mafft-fasttree \
  --i-sequences $rawdir/paired-pseudo-reps-seq-"$i".qza \
  --o-alignment $rawdir/aligned-rep-seqs-paired-pseudo-"$i".qza \
  --o-masked-alignment $rawdir/masked-aligned-rep-seqs-paired-pseudo-"$i".qza \
  --o-tree $rawdir/unrooted-tree-pseudo-"$i".qza \
  --o-rooted-tree $rawdir/rooted-tree-pseudo-"$i".qza

done