#!/bin/bash
#SBATCH -t 12:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --export=NONE
./single_job

module load QIIME2/2019.7

#Have to MERGE Run1 and Run2 to get pairwise comparison

qiime feature-table merge \
  --i-tables /data/mramseylab/raw_reads/2018_Serum/Run1/denoise-table-Run1.qza \
  --i-tables /data/mramseylab/raw_reads/2018_Serum/Run2/denoise-table-Run2.qza \
  --o-merged-table /data/mramseylab/raw_reads/2018_Serum/Run1-2_merge/table-single_Run12.qza

qiime feature-table merge-seqs \
  --i-data /data/mramseylab/raw_reads/2018_Serum/Run1/rep-seqs-Run1.qza \
  --i-data /data/mramseylab/raw_reads/2018_Serum/Run2/rep-seqs-Run2.qza \
  --o-merged-data /data/mramseylab/raw_reads/2018_Serum/Run1-2_merge/rep-seqs-Run12.qza

#Now run through the next steps

qiime feature-table summarize \
  --i-table /data/mramseylab/raw_reads/2018_Serum/Run1-2_merge/table-single_Run12.qza \
  --o-visualization /data/mramseylab/visualizations/table-Run12.qzv \
  --m-sample-metadata-file /data/mramseylab/metadata/Serum3.tsv

qiime feature-table tabulate-seqs \
  --i-data /data/mramseylab/raw_reads/2018_Serum/Run1-2_merge/rep-seqs-Run12.qza \
  --o-visualization /data/mramseylab/visualizations/rep-seqs-Run12.qzv

qiime phylogeny align-to-tree-mafft-fasttree \
  --i-sequences /data/mramseylab/raw_reads/2018_Serum/Run1-2_merge/rep-seqs-Run12.qza \
  --o-alignment /data/mramseylab/raw_reads/2018_Serum/Run1-2_merge/aligned-rep-seqs-Run12.qza \
  --o-masked-alignment /data/mramseylab/raw_reads/2018_Serum/Run1-2_merge/masked-aligned-rep-seqs-Run12.qza \
  --o-tree /data/mramseylab/raw_reads/2018_Serum/Run1-2_merge/unrooted-tree-Run12.qza \
  --o-rooted-tree /data/mramseylab/raw_reads/2018_Serum/Run1-2_merge/rooted-tree-Run12.qza