#!/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 tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path /data/mramseylab/raw_reads/2018_Serum/Run1 \
  --input-format CasavaOneEightSingleLanePerSampleDirFmt \
  --output-path /data/mramseylab/raw_reads/2018_Serum/Run1/demux-paired-end-1.qza

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path /data/mramseylab/raw_reads/2018_Serum/Run2 \
  --input-format CasavaOneEightSingleLanePerSampleDirFmt \
  --output-path /data/mramseylab/raw_reads/2018_Serum/Run2/demux-paired-end-2.qza

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path /data/mramseylab/raw_reads/2018_Serum/Runcomb \
  --input-format CasavaOneEightSingleLanePerSampleDirFmt \
  --output-path /data/mramseylab/raw_reads/2018_Serum/Runcomb/demux-paired-end-3.qza

qiime demux summarize \
  --i-data /data/mramseylab/raw_reads/2018_Serum/Run1/demux-paired-end-1.qza \
  --o-visualization /data/mramseylab/visualizations/demux-1.qzv

qiime demux summarize \
  --i-data /data/mramseylab/raw_reads/2018_Serum/Run2/demux-paired-end-2.qza \
  --o-visualization /data/mramseylab/visualizations/demux-2.qzv

qiime demux summarize \
  --i-data /data/mramseylab/raw_reads/2018_Serum/Runcomb/demux-paired-end-3.qza \
  --o-visualization /data/mramseylab/visualizations/demux-3.qzv