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

module load QIIME2/2019.7


qiime feature-table summarize \
  --i-table /data/mramseylab/raw_reads/2018_Serum/Run1/denoise-table-Run1.qza \
  --o-visualization /data/mramseylab/visualizations/table-Run1.qzv \
  --m-sample-metadata-file /data/mramseylab/metadata/Serum.tsv

qiime feature-table summarize \
  --i-table /data/mramseylab/raw_reads/2018_Serum/Run2/denoise-table-Run2.qza \
  --o-visualization /data/mramseylab/visualizations/table-Run2.qzv \
  --m-sample-metadata-file /data/mramseylab/metadata/Serum.tsv

qiime feature-table summarize \
  --i-table /data/mramseylab/raw_reads/2018_Serum/Runcomb/denoise-table-Run3.qza \
  --o-visualization /data/mramseylab/visualizations/table-Run3.qzv \
  --m-sample-metadata-file /data/mramseylab/metadata/Serum2.tsv

qiime feature-table tabulate-seqs \
  --i-data /data/mramseylab/raw_reads/2018_Serum/Run1/rep-seqs-Run1.qza \
  --o-visualization /data/mramseylab/visualizations/rep-seqs-Run1.qzv

qiime feature-table tabulate-seqs \
  --i-data /data/mramseylab/raw_reads/2018_Serum/Run2/rep-seqs-Run2.qza \
  --o-visualization /data/mramseylab/visualizations/rep-seqs-Run2.qzv

qiime feature-table tabulate-seqs \
  --i-data /data/mramseylab/raw_reads/2018_Serum/Runcomb/rep-seqs-Run3.qza \
  --o-visualization /data/mramseylab/visualizations/rep-seqs-Run3.qzv

qiime metadata tabulate \
  --m-input-file /data/mramseylab/raw_reads/2018_Serum/Run1/denoise-table-Run1.qza \
  --o-visualization /data/mramseylab/visualizations/denoising-stats-Run1.qzv

qiime metadata tabulate \
  --m-input-file /data/mramseylab/raw_reads/2018_Serum/Run2/denoise-table-Run2.qza \
  --o-visualization /data/mramseylab/visualizations/denoising-stats-Run2.qzv

qiime metadata tabulate \
  --m-input-file /data/mramseylab/raw_reads/2018_Serum/Runcomb/denoise-table-Run3.qza \
  --o-visualization /data/mramseylab/visualizations/denoising-stats-Run3.qzv

qiime phylogeny align-to-tree-mafft-fasttree \
  --i-sequences /data/mramseylab/raw_reads/2018_Serum/Run1/rep-seqs-Run1.qza \
  --o-alignment /data/mramseylab/raw_reads/2018_Serum/Run1/aligned-rep-seqs-Run1.qza \
  --o-masked-alignment /data/mramseylab/raw_reads/2018_Serum/Run1/masked-aligned-rep-seqs-Run1.qza \
  --o-tree /data/mramseylab/raw_reads/2018_Serum/Run1/unrooted-tree-Run1.qza \
  --o-rooted-tree /data/mramseylab/raw_reads/2018_Serum/Run1/rooted-tree-Run1.qza

qiime phylogeny align-to-tree-mafft-fasttree \
  --i-sequences /data/mramseylab/raw_reads/2018_Serum/Run2/rep-seqs-Run2.qza \
  --o-alignment /data/mramseylab/raw_reads/2018_Serum/Run2/aligned-rep-seqs-Run2.qza \
  --o-masked-alignment /data/mramseylab/raw_reads/2018_Serum/Run2/masked-aligned-rep-seqs-Run2.qza \
  --o-tree /data/mramseylab/raw_reads/2018_Serum/Run2/unrooted-tree-Run2.qza \
  --o-rooted-tree /data/mramseylab/raw_reads/2018_Serum/Run2/rooted-tree-Run2.qza

qiime phylogeny align-to-tree-mafft-fasttree \
  --i-sequences /data/mramseylab/raw_reads/2018_Serum/Runcomb/rep-seqs-Run3.qza \
  --o-alignment /data/mramseylab/raw_reads/2018_Serum/Runcomb/aligned-rep-seqs-Run3.qza \
  --o-masked-alignment /data/mramseylab/raw_reads/2018_Serum/Runcomb/masked-aligned-rep-seqs-Run3.qza \
  --o-tree /data/mramseylab/raw_reads/2018_Serum/Runcomb/unrooted-tree-Run3.qza \
  --o-rooted-tree /data/mramseylab/raw_reads/2018_Serum/Runcomb/rooted-tree-Run3.qza