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

module load QIIME2/2019.7

#Filter human associated reads.

qiime feature-table filter-samples \
  --i-table /data/mramseylab/raw_reads/2018_Serum/Run1-2_merge/table-single_Run12.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum3.tsv \
  --p-where "[Source]='Human'" \
  --o-filtered-table /data/mramseylab/proc_reads/filtered/RunM-Human-table.qza

qiime feature-table filter-features \
  --i-table /data/mramseylab/proc_reads/filtered/RunM-Human-table.qza \
  --m-metadata-file /data/mramseylab/classifiers/taxonomy.qza \
  --o-filtered-table /data/mramseylab/proc_reads/filtered/RunM-Human-table2.qza

qiime taxa barplot \
  --i-table /data/mramseylab/proc_reads/filtered/RunM-Human-table2.qza \
  --i-taxonomy /data/mramseylab/classifiers/taxonomy.qza \
  --m-metadata-file /data/mramseylab/metadata/Serum3.tsv \
  --o-visualization /data/mramseylab/proc_reads/core-metrics-results-RunM/Human-filtered-bar-plots2.qzv