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

module load QIIME2/2019.7

qiime diversity core-metrics-phylogenetic \
  --i-phylogeny /data/mramseylab/raw_reads/2018_Serum/Run1-2_merge/rooted-tree-Run12.qza \
  --i-table  /data/mramseylab/raw_reads/2018_Serum/Run1-2_merge/table-single_Run12.qza \
  --p-sampling-depth 20106 \
  --m-metadata-file /data/mramseylab/metadata/Serum.tsv \
  --output-dir /data/mramseylab/proc_reads/core-metrics-results-Run12

qiime diversity alpha-group-significance \
  --i-alpha-diversity /data/mramseylab/proc_reads/core-metrics-results-Run12/faith_pd_vector.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum.tsv \
  --o-visualization /data/mramseylab/proc_reads/core-metrics-results-Run12/faith-pd-group-significance.qzv

qiime diversity alpha-group-significance \
  --i-alpha-diversity /data/mramseylab/proc_reads/core-metrics-results-Run12/evenness_vector.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum.tsv \
  --o-visualization /data/mramseylab/proc_reads/core-metrics-results-Run12/evenness-group-significance.qzv

qiime diversity beta-group-significance \
  --i-distance-matrix /data/mramseylab/proc_reads/core-metrics-results-Run12/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file  /data/mramseylab/metadata/Serum.tsv \
  --m-metadata-column Condition \
  --o-visualization /data/mramseylab/proc_reads/core-metrics-results-Run12/unweighted-unifrac-Condition-significance.qzv \
  --p-pairwise

qiime diversity beta-group-significance \
  --i-distance-matrix /data/mramseylab/proc_reads/core-metrics-results-Run12/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum.tsv \
  --m-metadata-column Run \
  --o-visualization /data/mramseylab/proc_reads/core-metrics-results-Run12/unweighted-unifrac-Run-significance.qzv \
  --p-pairwise