#!/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 dada2 denoise-single \
  --i-demultiplexed-seqs /data/mramseylab/raw_reads/2018_Serum/Run1/demux-paired-end-1.qza \
  --p-trim-left 13 \
  --p-trunc-len 250 \
  --o-table /data/mramseylab/raw_reads/2018_Serum/Run1/denoise-table-Run1.qza \
  --o-representative-sequences /data/mramseylab/raw_reads/2018_Serum/Run1/rep-seqs-Run1.qza \
  --o-denoising-stats /data/mramseylab/raw_reads/2018_Serum/Run1/denoising-stats-Run1.qza

qiime dada2 denoise-single \
  --i-demultiplexed-seqs /data/mramseylab/raw_reads/2018_Serum/Run2/demux-paired-end-2.qza \
  --p-trim-left 13 \
  --p-trunc-len 250 \
  --o-table /data/mramseylab/raw_reads/2018_Serum/Run2/denoise-table-Run2.qza \
  --o-representative-sequences /data/mramseylab/raw_reads/2018_Serum/Run2/rep-seqs-Run2.qza \
  --o-denoising-stats /data/mramseylab/raw_reads/2018_Serum/Run2/denoising-stats-Run2.qza

qiime dada2 denoise-single \
  --i-demultiplexed-seqs /data/mramseylab/raw_reads/2018_Serum/Runcomb/demux-paired-end-3.qza \
  --p-trim-left 13 \
  --p-trunc-len 250 \
  --o-table /data/mramseylab/raw_reads/2018_Serum/Runcomb/denoise-table-Run3.qza \
  --o-representative-sequences /data/mramseylab/raw_reads/2018_Serum/Runcomb/rep-seqs-Run3.qza \
  --o-denoising-stats /data/mramseylab/raw_reads/2018_Serum/Runcomb/denoising-stats-Run3.qza