#Creating a symbolic link
ln -s /mnt/datasets/project_1/mouse_tutorial/demultiplexed_seqs /data/mouse_tutorial/demultiplexed_seqs

###Importing and demultiplexing
#Import data using the manifest format
qiime tools import \
  --type "SampleData[SequencesWithQuality]" \
  --input-format SingleEndFastqManifestPhred33V2 \
  --input-path /mnt/datasets/project_2/hiseas/hiseas_manifest.txt \
  --output-path ./demux_seqs.qza

#Summarize the demultiplexed sequences to generate a visualization file
qiime demux summarize \
  --i-data ./demux_seqs.qza \
  --o-visualization ./demux_seqs.qzv

#Denoise the demultiplexed sequences with DADA2 at truncation length 291
qiime dada2 denoise-single \
  --i-demultiplexed-seqs ./demux_seqs.qza \
  --p-trim-left 0 \
  --p-trunc-len 291 \
  --o-representative-sequences ./rep-seqs_291.qza \
  --o-table ./table_291.qza \
  --o-denoising-stats ./stats_291.qza
  
#Tabulate the denoising statistics to generate a visualization file
qiime metadata tabulate \
  --m-input-file ./stats_291.qza \
  --o-visualization ./stats_291.qzv
  
#Summarize the features table to generate a visualization file 
qiime feature-table summarize \
  --i-table ./table_291.qza \
  --o-visualization ./table_291.qzv \
  --m-sample-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt
  
#Tabulate the representative sequences to generate a visualization file
qiime feature-table tabulate-seqs \
  --i-data ./rep-seqs_291.qza \
  --o-visualization ./rep-seqs_291.qzv

###Filtration by body site    
# Filter features table by skin samples
qiime feature-table filter-samples \
  --i-table table_291.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --p-where "[sample_type]= 'skin'" \
  --o-filtered-table skin-filtered-table.qza

# Generate visualization file of skin filtered table
qiime feature-table summarize \
  --i-table skin-filtered-table.qza \
  --o-visualization skin-filtered-table.qzv \
  --m-sample-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt

###Alpha rarefaction of skin filtered data
qiime diversity alpha-rarefaction \
  --i-table skin-filtered-table.qza \
  --p-max-depth 60000\
  --m-metadata-file hiseas_metadata2.txt \
  --o-visualization alpha-rarefaction.qzv

###Taxonomy Analysis
#Assign taxonomy using Naive Bayes Classifier pre-trained with Silva 138 99% OTUs
qiime feature-classifier classify-sklearn \
  --i-reads ./rep-seqs_291.qza \
  --i-classifier /mnt/datasets/classifiers/silva-138-99-515-806-nb-classifier.qza \
  --o-classification ./taxonomy.qza

###Filtration
#Remove mitochondrial sequences from the skin filtered table
qiime taxa filter-table \
--i-table ./skin-filtered-table.qza \
--i-taxonomy ./taxonomy.qza \
--p-exclude mitochondria \
--o-filtered-table ./skin-filtered-table-rare-mito.qza

#Generate visualization file of table filtered for mitochondria
qiime feature-table summarize \
  --i-table ./skin-filtered-table-rare.qza \
  --o-visualization skin-filtered-table-rare.qzv \
  --m-sample-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt

qiime feature-table summarize \
  --i-table ./skin-filtered-table-rare-mito.qza \
  --o-visualization skin-filtered-table-rare-mito.qzv \
  --m-sample-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt

###Phylogenetic analysis
qiime phylogeny align-to-tree-mafft-fasttree \
  --i-sequences rep-seqs_291.qza \
  --o-alignment aligned-rep-seqs.qza \
  --o-masked-alignment masked-aligned-rep-seqs.qza \
  --o-tree unrooted-tree.qza \
  --o-rooted-tree rooted-tree.qza


###Diversity metrics for all timestamps
#Diversity analysis core metrics at sampling depth 15720
qiime diversity core-metrics-phylogenetic \
  --i-table skin-filtered-table-rare-mito.qza \
  --i-phylogeny rooted-tree.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --p-sampling-depth 15720 \
  --output-dir skin-rare-mito-core-metrics-results

#Calculate alpha group significance with each alpha diversity metric
#Faith's phylogenetic distance
qiime diversity alpha-group-significance \
  --i-alpha-diversity skin-rare-mito-core-metrics-results/faith_pd_vector.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --o-visualization skin-rare-mito-core-metrics-results/skin-rare-mito-faiths_pd_statistics.qzv

#Peilou's evenness
qiime diversity alpha-group-significance \
  --i-alpha-diversity skin-rare-mito-core-metrics-results/evenness_vector.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --o-visualization skin-rare-mito-core-metrics-results/skin-rare-mito-evenness_statistics.qzv

#Observed features
qiime diversity alpha-group-significance \
  --i-alpha-diversity skin-rare-mito-core-metrics-results/observed_features_vector.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --o-visualization skin-rare-mito-core-metrics-results/skin-rare-mito-observed_statistics.qzv

#Shannon diversity 
qiime diversity alpha-group-significance \
  --i-alpha-diversity skin-rare-mito-core-metrics-results/shannon_vector.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --o-visualization skin-rare-mito-core-metrics-results/skin-rare-mito-shannon_statistics.qzv

#Calculate beta group significance with each beta diversity metric by crew_id
#Unweighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix skin-rare-mito-core-metrics-results/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_id \
  --o-visualization skin-rare-mito-core-metrics-results/skin-rare-mito-unweighted-unifrac-significance.qzv \
  --p-pairwise

#Weighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix skin-rare-mito-core-metrics-results/weighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_id \
  --o-visualization skin-rare-mito-core-metrics-results/skin-rare-mito-weighted-unifrac-significance.qzv \
  --p-pairwise

#Jaccard distance
qiime diversity beta-group-significance \
  --i-distance-matrix skin-rare-mito-core-metrics-results/jaccard_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_id \
  --o-visualization skin-rare-mito-core-metrics-results/skin-rare-mito-jaccard-significance.qzv \
  --p-pairwise

#Bray-Curtis distance
qiime diversity beta-group-significance \
  --i-distance-matrix skin-rare-mito-core-metrics-results/bray_curtis_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_id \
  --o-visualization skin-rare-mito-core-metrics-results/skin-rare-mito-bray-significance.qzv \
  --p-pairwise

#Calculate beta group significance with each beta diversity metric by crew_interaction
#Unweighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix skin-rare-mito-core-metrics-results/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_interaction \
  --o-visualization skin-rare-mito-core-metrics-results/srm-interaction-unweighted-unifrac-significance.qzv \
  --p-pairwise

#Weighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix skin-rare-mito-core-metrics-results/weighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_interaction \
  --o-visualization skin-rare-mito-core-metrics-results/srm-interaction-weighted-unifrac-significance.qzv \
  --p-pairwise

#Jaccard distance
qiime diversity beta-group-significance \
  --i-distance-matrix skin-rare-mito-core-metrics-results/jaccard_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_interaction \
  --o-visualization skin-rare-mito-core-metrics-results/srm-interaction-jaccard-significance.qzv \
  --p-pairwise

#Bray-Curtis distance
qiime diversity beta-group-significance \
  --i-distance-matrix skin-rare-mito-core-metrics-results/bray_curtis_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_interaction \
  --o-visualization skin-rare-mito-core-metrics-results/srm-interaction-bray-significance.qzv \
  --p-pairwise

###Filtration by timestamps
#Baseline (04Sept15)
qiime feature-table filter-samples \
--i-table skin-filtered-table-rare-mito.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --p-where "[collection_timestamp]= '2015-09-04'" \
  --o-filtered-table filtered-baseline-table.qza

qiime feature-table summarize \
  --i-table filtered-baseline-table.qza \
  --o-visualization filtered-baseline-table.qzv \
  --m-sample-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt

#Final Timepoint (05Oct16)
qiime feature-table filter-samples \
--i-table skin-filtered-table-rare-mito.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --p-where "[collection_timestamp]= '2016-08-05'" \
  --o-filtered-table filtered-final-table.qza

qiime feature-table summarize \
  --i-table filtered-final-table.qza \
  --o-visualization filtered-final-table.qzv \
  --m-sample-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt

#04Sept15; 16Oct15; 27Nov15
 qiime feature-table filter-samples \
  --i-table skin-filtered-table-rare-mito.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --p-where "[collection_timestamp] IN ('2015-09-04', '2015-10-16', '2015-11-27')" \
  --o-filtered-table filtered-1-table.qza

qiime feature-table summarize \
  --i-table filtered-1-table.qza \
  --o-visualization filtered-1-table.qzv \
  --m-sample-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt

#08Jan16; 19Feb16; 01Apr16
 qiime feature-table filter-samples \
  --i-table skin-filtered-table-rare-mito.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --p-where "[collection_timestamp] IN ('2016-01-08', '2016-02-19', '2016-04-01')" \
  --o-filtered-table filtered-2-table.qza

qiime feature-table summarize \
  --i-table filtered-2-table.qza \
  --o-visualization filtered-2-table.qzv \
  --m-sample-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt

#13May16; 24Jun16; 05Aug16
 qiime feature-table filter-samples \
  --i-table skin-filtered-table-rare-mito.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --p-where "[collection_timestamp] IN ('2016-05-13', '2016-06-24', '2016-08-05')" \
  --o-filtered-table filtered-3-table.qza

qiime feature-table summarize \
  --i-table filtered-3-table.qza \
  --o-visualization filtered-3-table.qzv \
  --m-sample-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt

###TAXONOMY ANALYSIS
#Taxa barplot of skin samples at baseline
qiime feature-table filter-samples \
  --i-table ./filtered-baseline-table.qza \
  --p-min-frequency 15720 \
  --o-filtered-table ./table-barplot-15k.qza

qiime taxa barplot \
  --i-table ./table-barplot-15k.qza \
  --i-taxonomy ./taxonomy.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --o-visualization ./taxa-barplot-15k.qzv

#Taxa barplot of skin samples at final timestamp
qiime feature-table filter-samples \
  --i-table ./filtered-final-table.qza \
  --p-min-frequency 15720 \
  --o-filtered-table ./table-barplot-final-15k.qza

qiime taxa barplot \
  --i-table ./table-barplot-final-15k.qza \
  --i-taxonomy ./taxonomy.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --o-visualization ./taxa-barplot-final-15k.qzv

###Diversity metrics of interest at each timestamp: alpha (Evenness, PD); beta (Unweighted, Weighted)
#Group1: 04Sept15; 16Oct15; 27Nov15
#Diversity Analysis core metrics at sampling depth 15720
qiime diversity core-metrics-phylogenetic \
  --i-table filtered-1-table.qza \
  --i-phylogeny rooted-tree.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --p-sampling-depth 15720 \
  --output-dir group1-core-metrics-results

#Calculate alpha group significance with each alpha diversity metric
#Faith's phylogenetic distance
qiime diversity alpha-group-significance \
  --i-alpha-diversity group1-core-metrics-results/faith_pd_vector.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --o-visualization group1-core-metrics-results/group1-faiths_pd_statistics.qzv

#Peilou's evenness
qiime diversity alpha-group-significance \
  --i-alpha-diversity group1-core-metrics-results/evenness_vector.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --o-visualization group1-core-metrics-results/group1-evenness_statistics.qzv

#Calculate beta group significance with each beta diversity metric by crew_id
#Unweighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix group1-core-metrics-results/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_id \
  --o-visualization group1-core-metrics-results/crewid-group1-unweighted-unifrac-significance.qzv \
  --p-pairwise

# Weighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix group1-core-metrics-results/weighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_id \
  --o-visualization group1-core-metrics-results/crewid-group1-weighted-unifrac-significance.qzv \
  --p-pairwise

#Calculate beta group significance with each beta diversity metric by crew_interaction
#Unweighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix group1-core-metrics-results/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_interaction \
  --o-visualization group1-core-metrics-results/interaction-group1-unweighted-unifrac-significance.qzv \
  --p-pairwise

#Weighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix group1-core-metrics-results/weighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_interaction \
  --o-visualization group1-core-metrics-results/interaction-group1-weighted-unifrac-significance.qzv \
  --p-pairwise

#Group2: 08Jan16; 19Feb16; 01Apr16
#Diversity Analysis core metrics at sampling depth 15720
qiime diversity core-metrics-phylogenetic \
  --i-table filtered-2-table.qza \
  --i-phylogeny rooted-tree.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --p-sampling-depth 15720 \
  --output-dir group2-core-metrics-results

#Calculate alpha group significance with each alpha diversity metric
#Faith's phylogenetic distance
qiime diversity alpha-group-significance \
  --i-alpha-diversity group2-core-metrics-results/faith_pd_vector.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --o-visualization group2-core-metrics-results/group2-faiths_pd_statistics.qzv

#Peilou's evenness
qiime diversity alpha-group-significance \
  --i-alpha-diversity group2-core-metrics-results/evenness_vector.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --o-visualization group2-core-metrics-results/group2-evenness_statistics.qzv

#Calculate beta group significance with each beta diversity metric by crew_id
#Unweighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix group2-core-metrics-results/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_id \
  --o-visualization group2-core-metrics-results/crewid-group2-unweighted-unifrac-significance.qzv \
  --p-pairwise

#Weighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix group2-core-metrics-results/weighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_id \
  --o-visualization group2-core-metrics-results/crewid-group2-weighted-unifrac-significance.qzv \
  --p-pairwise

#Calculate beta group significance with each beta diversity metric by crew_interaction
#Unweighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix group2-core-metrics-results/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_interaction \
  --o-visualization group2-core-metrics-results/interaction-group2-unweighted-unifrac-significance.qzv \
  --p-pairwise

#Weighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix group2-core-metrics-results/weighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_interaction \
  --o-visualization group2-core-metrics-results/interaction-group2-weighted-unifrac-significance.qzv \
  --p-pairwise

#13May16; 26Jun16; 05Oct16
#Diversity Analysis core metrics at sampling depth 15720
qiime diversity core-metrics-phylogenetic \
  --i-table filtered-3-table.qza \
  --i-phylogeny rooted-tree.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --p-sampling-depth 15720 \
  --output-dir group3-core-metrics-results

#Calculate alpha group significance with each alpha diversity metric
#Faith's phylogenetic distance
qiime diversity alpha-group-significance \
  --i-alpha-diversity group3-core-metrics-results/faith_pd_vector.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --o-visualization group3-core-metrics-results/group3-faiths_pd_statistics.qzv

#Peilou's evenness
qiime diversity alpha-group-significance \
  --i-alpha-diversity group3-core-metrics-results/evenness_vector.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --o-visualization group3-core-metrics-results/group3-evenness_statistics.qzv

#Calculate beta group significance with each beta diversity metric by crew_id
#Unweighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix group3-core-metrics-results/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_id \
  --o-visualization group3-core-metrics-results/crewid-group3-unweighted-unifrac-significance.qzv \
  --p-pairwise

#Weighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix group3-core-metrics-results/weighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_id \
  --o-visualization group3-core-metrics-results/crewid-group3-weighted-unifrac-significance.qzv \
  --p-pairwise

#Calculate beta group significance with each beta diversity metric by crew_interaction
#Unweighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix group3-core-metrics-results/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_interaction \
  --o-visualization group3-core-metrics-results/interaction-group3-unweighted-unifrac-significance.qzv \
  --p-pairwise

#Weighted UniFrac distance
qiime diversity beta-group-significance \
  --i-distance-matrix group3-core-metrics-results/weighted_unifrac_distance_matrix.qza \
  --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
  --m-metadata-column crew_interaction \
  --o-visualization group3-core-metrics-results/interaction-group3-weighted-unifrac-significance.qzv \
  --p-pairwise

###Longitudinal graphs
#Alpha diversity
qiime longitudinal volatility \
     --m-metadata-file /mnt/datasets/project_2/hiseas/hiseas_metadata.txt \
     --m-metadata-file evenness_vector.qza \
     --p-default-metric pielou_evenness \
     --p-default-group-column crew_interaction \
     --p-state-column time_sampling_days \
     --p-individual-id-column crew_id \
     --o-visualization alpha-volatility.qzv

#Beta diversity
#Note: We had to create a custom metadata file that contained just the crew member #samples (hiseas_metadata_crew.txt)
qiime longitudinal first-distances \
  --i-distance-matrix weighted_unifrac_distance_matrix.qza \
  --m-metadata-file /data/hiseas/hiseas_metadata_crew.txt \
  --p-state-column time_sampling_days \
  --p-individual-id-column crew_id \
  --p-replicate-handling random \
  --o-first-distances first-distances-wunifrac.qza

qiime longitudinal volatility \
     --m-metadata-file /data/hiseas/hiseas_metadata_crew.txt \
     --m-metadata-file first-distances-wunifrac.qza \
     --p-default-metric Distance \
     --p-default-group-column crew_interaction \
     --p-state-column time_sampling_days \
     --p-individual-id-column crew_id \
     --o-visualization beta-volatility.qzv

qiime longitudinal volatility \
     --m-metadata-file /data/hiseas/hiseas_metadata_crew.txt \
     --m-metadata-file weighted_unifrac_pcoa_results.qza \
     --p-default-metric Distance \
     --p-default-group-column crew_interaction \
     --p-state-column time_sampling_days \
     --p-individual-id-column crew_id \
     --o-visualization beta-volatility-wunifrac-pcoa.qzv

###Longitudinal ANOVA Q2
qiime longitudinal anova \
  --m-metadata-file first-distances-wunifrac.qza \
  --m-metadata-file /data/hiseas/hiseas_metadata_crew.txt \
  --p-formula 'Distance ~ crew_id * crew_interaction' \
  --o-visualization wunifrac_anova.qzv

###QIIME Export
#Exporting taxonomy as biom file
qiime tools export \
--input-path taxonomy.qza \
--output-path skin-exported

#Exporting tree as nwk file
qiime tools export \
--input-path rooted-tree.qza \
--output-path skin-exported

#Export the features table for each collection of timestamps (group_1, group_2, group_3)
qiime tools export \
--input-path filtered-1-table.qza \
--output-path group1-exported

qiime tools export \
--input-path filtered-2-table.qza \
--output-path group2-exported 

qiime tools export \
--input-path filtered-3-table.qza \
--output-path group3-exported 

#Export the features table for overall timestamps
qiime tools export \
--input-path skin-filtered-table-rare-mito.qza \
--output-path skin-exported

# Manually edit column names of exported taxonomy file using nano
  # 'Feature ID' to '#OTUID'
  # 'Taxon' to 'taxonomy'
  # 'Confidence' to 'confidence'
nano skin-exported/taxonomy.tsv

# Combine taxonomy with BIOM data for skin overall, group1, group2, group3
biom add-metadata \
-i skin-exported/feature-table.biom \
-o skin-exported/overall-table-with-taxonomy.biom \
--observation-metadata-fp skin-exported/taxonomy.tsv \
--sc-separated taxonomy

biom add-metadata \
-i group1-exported/feature-table.biom \
-o skin-exported/group1-table-with-taxonomy.biom \
--observation-metadata-fp skin-exported/taxonomy.tsv \
--sc-separated taxonomy

biom add-metadata \
-i group2-exported/feature-table.biom \
-o skin-exported/group2-table-with-taxonomy.biom \
--observation-metadata-fp skin-exported/taxonomy.tsv \
--sc-separated taxonomy

biom add-metadata \
-i group3-exported/feature-table.biom \
-o skin-exported/group3-table-with-taxonomy.biom \
--observation-metadata-fp skin-exported/taxonomy.tsv \
--sc-separated taxonomy