#!/bin/bash
#SBATCH -t 2:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=24g
#SBATCH --export=NONE
#SBATCH --mail-user=mramsey@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL
#./D2merge.sh

module load QIIME2/2019.7

for d in /data/mramseylab/raw_reads/2018_Serum/Run* ;
do
SUFX=${d#*Run}

qiime dada2 denoise-single \
  --i-demultiplexed-seqs /data/mramseylab/raw_reads/2018_Serum/Run$SUFX/demux-$SUFX.qza \
  --p-trim-left 13 \
  --p-trunc-len 250 \
  --o-table /data/mramseylab/raw_reads/2018_Serum/Run$SUFX/denoise-table-$SUFX.qza \
  --o-representative-sequences /data/mramseylab/raw_reads/2018_Serum/Run$SUFX/rep-seqs-$SUFX.qza \
  --o-denoising-stats /data/mramseylab/raw_reads/2018_Serum/Run$SUFX/denoising-stats-$SUFX.qza

done
#Have to MERGE Run1 and Run2 to get pairwise comparison
#Must make directory before running below else it will error out.

mkdir /data/mramseylab/raw_reads/2018_Serum/Merge_runs/

qiime feature-table merge \
  --i-tables /data/mramseylab/raw_reads/2018_Serum/Run1/denoise-table-1.qza \
  --i-tables /data/mramseylab/raw_reads/2018_Serum/Run2/denoise-table-2.qza \
  --o-merged-table /data/mramseylab/raw_reads/2018_Serum/Merge_runs/denoise-table-merge.qza

qiime feature-table merge-seqs \
  --i-data /data/mramseylab/raw_reads/2018_Serum/Run1/rep-seqs-1.qza \
  --i-data /data/mramseylab/raw_reads/2018_Serum/Run2/rep-seqs-2.qza \
  --o-merged-data /data/mramseylab/raw_reads/2018_Serum/Merge_runs/rep-seqs-merge.qza

qiime feature-table summarize \
  --i-table /data/mramseylab/raw_reads/2018_Serum/Merge_runs/denoise-table-merge.qza \
  --o-visualization /data/mramseylab/visualizations/denoise-table-merge.qzv \
  --m-sample-metadata-file /data/mramseylab/metadata/Serum5.tsv

qiime feature-table tabulate-seqs \
  --i-data /data/mramseylab/raw_reads/2018_Serum/Merge_runs/rep-seqs-merge.qza \
  --o-visualization /data/mramseylab/visualizations/rep-seqs-merge.qzv

qiime phylogeny align-to-tree-mafft-fasttree \
  --i-sequences /data/mramseylab/raw_reads/2018_Serum/Merge_runs/rep-seqs-merge.qza \
  --o-alignment /data/mramseylab/raw_reads/2018_Serum/Merge_runs/aligned-rep-seqs-merge.qza \
  --o-masked-alignment /data/mramseylab/raw_reads/2018_Serum/Merge_runs/masked-aligned-rep-seqs-merge.qza \
  --o-tree /data/mramseylab/raw_reads/2018_Serum/Merge_runs/unrooted-tree-merge.qza \
  --o-rooted-tree /data/mramseylab/raw_reads/2018_Serum/Merge_runs/rooted-tree-merge.qza