#!/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/rooted-tree-Run1.qza \
  --i-table  /data/mramseylab/raw_reads/2018_Serum/Run1/denoise-table-Run1.qza \
  --p-sampling-depth 2944 \
  --m-metadata-file /data/mramseylab/metadata/Serum.tsv \
  --output-dir /data/mramseylab/proc_reads/core-metrics-results-Run1

qiime diversity core-metrics-phylogenetic \
  --i-phylogeny /data/mramseylab/raw_reads/2018_Serum/Run2/rooted-tree-Run2.qza \
  --i-table  /data/mramseylab/raw_reads/2018_Serum/Run2/denoise-table-Run2.qza \
  --p-sampling-depth 1000 \
  --m-metadata-file /data/mramseylab/metadata/Serum.tsv \
  --output-dir /data/mramseylab/proc_reads/core-metrics-results-Run2

qiime diversity core-metrics-phylogenetic \
  --i-phylogeny /data/mramseylab/raw_reads/2018_Serum/Runcomb/rooted-tree-Run3.qza \
  --i-table  /data/mramseylab/raw_reads/2018_Serum/Runcomb/denoise-table-Run3.qza \
  --p-sampling-depth 4183 \
  --m-metadata-file /data/mramseylab/metadata/Serum2.tsv \
  --output-dir /data/mramseylab/proc_reads/core-metrics-results-Run3

qiime diversity alpha-group-significance \
  --i-alpha-diversity /data/mramseylab/proc_reads/core-metrics-results-Run1/faith_pd_vector.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum.tsv \
  --o-visualization /data/mramseylab/proc_reads/core-metrics-results-Run1/faith-pd-group-significance.qzv

qiime diversity alpha-group-significance \
  --i-alpha-diversity /data/mramseylab/proc_reads/core-metrics-results-Run2/faith_pd_vector.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum.tsv \
  --o-visualization /data/mramseylab/proc_reads/core-metrics-results-Run2/faith-pd-group-significance.qzv

qiime diversity alpha-group-significance \
  --i-alpha-diversity /data/mramseylab/proc_reads/core-metrics-results-Run3/faith_pd_vector.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum2.tsv \
  --o-visualization /data/mramseylab/proc_reads/core-metrics-results-Run3/faith-pd-group-significance.qzv

qiime diversity alpha-group-significance \
  --i-alpha-diversity /data/mramseylab/proc_reads/core-metrics-results-Run1/evenness_vector.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum.tsv \
  --o-visualization /data/mramseylab/proc_reads/core-metrics-results-Run1/evenness-group-significance.qzv

qiime diversity alpha-group-significance \
  --i-alpha-diversity /data/mramseylab/proc_reads/core-metrics-results-Run2/evenness_vector.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum.tsv \
  --o-visualization /data/mramseylab/proc_reads/core-metrics-results-Run2/evenness-group-significance.qzv

qiime diversity alpha-group-significance \
  --i-alpha-diversity /data/mramseylab/proc_reads/core-metrics-results-Run3/evenness_vector.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum2.tsv \
  --o-visualization /data/mramseylab/proc_reads/core-metrics-results-Run3/evenness-group-significance.qzv

qiime diversity beta-group-significance \
  --i-distance-matrix /data/mramseylab/proc_reads/core-metrics-results-Run1/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-Run1/unweighted-unifrac-Condition-significance.qzv \
  --p-pairwise

qiime diversity beta-group-significance \
  --i-distance-matrix /data/mramseylab/proc_reads/core-metrics-results-Run2/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-Run2/unweighted-unifrac-Condition-significance.qzv \
  --p-pairwise

qiime diversity beta-group-significance \
  --i-distance-matrix /data/mramseylab/proc_reads/core-metrics-results-Run3/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file  /data/mramseylab/metadata/Serum2.tsv \
  --m-metadata-column Condition \
  --o-visualization /data/mramseylab/proc_reads/core-metrics-results-Run3/unweighted-unifrac-Condition-significance.qzv \