#!/bin/bash
#SBATCH -t 4:00:00
#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

module load QIIME2/2019.7

rawdir=/data/mramseylab/raw_reads/2018_Serum/Merge_runs/
procdir=/data/mramseylab/proc_reads/
metadir=/data/mramseylab/metadata/
cmr="core-metrics-results"

qiime diversity core-metrics-phylogenetic \
  --i-phylogeny $rawdir\rooted-tree-merge.qza \
  --i-table  $rawdir\denoise-table-merge.qza \
  --p-sampling-depth 22000 \
  --m-metadata-file $metadir\Serum5.tsv \
  --output-dir $procdir$cmr\-initial

qiime diversity alpha-group-significance \
  --i-alpha-diversity $procdir$cmr\-initial/faith_pd_vector.qza \
  --m-metadata-file $metadir\Serum5.tsv \
  --o-visualization $procdir$cmr\-initial/faith-pd-group-significance.qzv

qiime diversity alpha-group-significance \
  --i-alpha-diversity $procdir$cmr\-initial/evenness_vector.qza \
  --m-metadata-file $metadir\Serum5.tsv \
  --o-visualization $procdir$cmr\-initial/evenness-group-significance.qzv

array=( unweighted_unifrac_distance_matrix weighted_unifrac_distance_matrix bray_curtis_distance_matrix )

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

qiime diversity beta-group-significance \
  --i-distance-matrix $procdir$cmr\-initial/$i.qza \
  --m-metadata-file  $metadir\Serum5.tsv \
  --m-metadata-column Condition \
  --o-visualization $procdir$cmr\-initial/$i.qzv \
  --p-pairwise

done