#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=24g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2019.7

subjects=( A J An S ) #creates a list of subjects to use

for i in "${subjects[@]}" #for variable (subject) in list, $ (open) list (subjects) use all in list ([@])
do

treein=/data/mramseylab/raw_reads/trip"$i"/rooted-tree-pseudo-"$i".qza
procdir=/data/mramseylab/raw_reads/trip"$i"/
metadir=/data/mramseylab/metadata/plaque_meta_"$i".tsv
filtdir=/data/mramseylab/raw_reads/trip"$i"/filter/denoise-pseudo_feat_2_feq_5-"$i".qza
cmr="core-metric-resultst-time-$i"
alpha="alpha-$i"

mkdir $procdir$alpha

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

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

qiime diversity alpha-group-significance \
--i-alpha-diversity $procdir$cmr/shannon_vector.qza \
--m-metadata-file $metadir \
--o-visualization $procdir$alpha/shannon-significance-"$i".qzv

done