# de_Leon_et_al_2022_Supplemental_shell_script.sh # # Captivity plays a role in shaping the gut microbiome of social mammals # #!/bin/bash # # ---------------------------------------------------- # Experiment: DLTY4721-007 # Date: 01-Mar-2022 # # # Import zoo dataset using the manifest file qiime tools import \ --type 'SampleData[SequencesWithQuality]' \ --input-path /mnt/datasets/project_2/zoo/zoo_manifest.txt \ --input-format SingleEndFastqManifestPhred33V2 \ --output-path demux.qza # # # Create visualization of demultiplexed samples qiime demux summarize \ --i-data demux.qza \ --o-visualization demux.qzv # # # Denoise and determine ASVs with DADA2 qiime dada2 denoise-single \ --i-demultiplexed-seqs demux.qza \ --p-trim-left 0 \ --p-trunc-len 150 \ --o-representative-sequences rep-seqs.qza \ --o-table table.qza \ --o-denoising-stats stats.qza # # # Visualize DADA2 stats qiime metadata tabulate \ --m-input-file stats.qza \ --o-visualization stats.qzv # # # Visualize ASVs stats qiime feature-table summarize \ --i-table table.qza \ --o-visualization table.qzv \ --m-sample-metadata-file /root/data/project_2/zoo_metadata_mod.tsv # qiime feature-table tabulate-seqs \ --i-data rep-seqs.qza \ --o-visualization rep-seqs.qzv # # # # Taxonomic analysis # # Classify representative sequences using a trained classifer that compares # sequences to 16SrRNA V3 & V4 regions qiime feature-classifier classify-sklearn \ --i-classifier /mnt/datasets/classifiers/gg-13-8-99-515-806-nb-classifier.qza \ --i-reads rep-seqs.qza \ --o-classification taxonomy.qza # qiime metadata tabulate \ --m-input-file taxonomy.qza \ --o-visualization taxonomy.qzv # # Taxonomy barplots qiime taxa barplot \ --i-table table.qza \ --i-taxonomy taxonomy.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization taxa-bar-plots.qzv # # # Filter out mitochrondria and chloroplast sequences qiime taxa filter-table \ --i-table table.qza \ --i-taxonomy taxonomy.qza \ --p-exclude mitochondria,chloroplast \ --o-filtered-table table-no-mitochondria-no-chloroplast.qza # # # Filter table to include only social animals qiime feature-table filter-samples \ --i-table table-no-mitochondria-no-chloroplast.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --p-where "[SocialityHMC] = 'Yes'" \ --o-filtered-table table-social.qza # # # Filter table to include only social animals that live in captivity qiime feature-table filter-samples \ --i-table table-social.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --p-where "[captive_wild] = 'captive'" \ --o-filtered-table table-social-cap.qza # # # Filter table to include only social animals that live in the wild qiime feature-table filter-samples \ --i-table table-social.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --p-where "[captive_wild] = 'wild'" \ --o-filtered-table table-social-wild.qza # # # Filter table to include only non-social animals qiime feature-table filter-samples \ --i-table table-no-mitochondria-no-chloroplast.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --p-where "[SocialityHMC] = 'No'" \ --o-filtered-table table-non-social.qza # # # Visualize ASVs stats for each subsetted table # no-mitochondria-no-chloroplast qiime feature-table summarize \ --i-table table-no-mitochondria-no-chloroplast.qza \ --o-visualization table-no-mitochondria-no-chloroplast.qzv \ --m-sample-metadata-file /root/data/project_2/zoo_metadata_mod.tsv # # social qiime feature-table summarize \ --i-table table-social.qza \ --o-visualization table-social.qzv \ --m-sample-metadata-file /root/data/project_2/zoo_metadata_mod.tsv # # social captive qiime feature-table summarize \ --i-table table-social-cap.qza \ --o-visualization table-social-cap.qzv \ --m-sample-metadata-file /root/data/project_2/zoo_metadata_mod.tsv # # social wild qiime feature-table summarize \ --i-table table-social-wild.qza \ --o-visualization table-social-wild.qzv \ --m-sample-metadata-file /root/data/project_2/zoo_metadata_mod.tsv # # non-social qiime feature-table summarize \ --i-table table-non-social.qza \ --o-visualization table-non-social.qzv \ --m-sample-metadata-file /root/data/project_2/zoo_metadata_mod.tsv # # # Diversity metrics # Generate a tree for phylogenetic diversity analyses qiime phylogeny align-to-tree-mafft-fasttree \ --i-sequences rep-seqs.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 # # # ---------------------------------------------------- # Experiment: DLTY4721-013 # Date: 09-Mar-2022 # # # Generate alpha-rarefaction curve using the max sampling depth for each table # table-social qiime diversity alpha-rarefaction \ --i-table table-social.qza \ --i-phylogeny rooted-tree.qza \ --p-max-depth 236017 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization alpha-rarefaction-social.qzv # # table-non-social qiime diversity alpha-rarefaction \ --i-table table-non-social.qza \ --i-phylogeny rooted-tree.qza \ --p-max-depth 161881 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization alpha-rarefaction-non-social.qzv # # table-social-cap qiime diversity alpha-rarefaction \ --i-table table-social-cap.qza \ --i-phylogeny rooted-tree.qza \ --p-max-depth 236017 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization alpha-rarefaction-social-cap.qzv # # table-social-wild qiime diversity alpha-rarefaction \ --i-table table-social-wild.qza \ --i-phylogeny rooted-tree.qza \ --p-max-depth 215988 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization alpha-rarefaction-social-wild.qzv # # #---------- # Diversty metrics generation # # Social animals: ## Calculate alpha and beta diversity metrics qiime diversity core-metrics-phylogenetic \ --i-phylogeny rooted-tree.qza \ --i-table table-social.qza \ --p-sampling-depth 103804 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --output-dir core-metrics-results-social # ## Calculate alpha-group-significance ### Faith's phylogenetic diversity qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-social/faith_pd_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-social/faith-pd-group-significance-social.qzv # ### Evenness qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-social/evenness_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-social/evenness-group-significance-social.qzv # ## Calculate beta-group-significance on the captive_wild metadata column qiime diversity beta-group-significance \ --i-distance-matrix core-metrics-results-social/unweighted_unifrac_distance_matrix.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --m-metadata-column captive_wild \ --o-visualization core-metrics-results-social/unweighted-unifrac-cap-wild-significance-social.qzv \ --p-pairwise # # # Non-social animals: ## Calculate alpha and beta diversity metrics qiime diversity core-metrics-phylogenetic \ --i-phylogeny rooted-tree.qza \ --i-table table-non-social.qza \ --p-sampling-depth 93885 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --output-dir core-metrics-results-non-social # ## Calculate alpha-group-significance ### Faith's phylogenetic diversity qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-non-social/faith_pd_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-non-social/faith-pd-group-significance-non-social.qzv # ### Evenness qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-non-social/evenness_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-non-social/evenness-group-significance-non-social.qzv # ## Calculate beta-group-significance on the captive_wild metadata column qiime diversity beta-group-significance \ --i-distance-matrix core-metrics-results-non-social/unweighted_unifrac_distance_matrix.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --m-metadata-column captive_wild \ --o-visualization core-metrics-results-non-social/unweighted-unifrac-cap-wild-significance-non-social.qzv \ --p-pairwise # # # Social animals living in captivity: ## Calculate alpha and beta diversity metrics qiime diversity core-metrics-phylogenetic \ --i-phylogeny rooted-tree.qza \ --i-table table-social-cap.qza \ --p-sampling-depth 98425 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --output-dir core-metrics-results-social-cap # ## Calculate alpha-group-significance ### Faith's phylogenetic diversity qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-social-cap/faith_pd_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-social-cap/faith-pd-group-significance-social-cap.qzv # ### Evenness qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-social-cap/evenness_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-social-cap/evenness-group-significance-social-cap.qzv # ## Calculate beta-group-significance on the SocialGrpSizeCat metadata column qiime diversity beta-group-significance \ --i-distance-matrix core-metrics-results-social-cap/unweighted_unifrac_distance_matrix.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --m-metadata-column SocialGrpSizeCat \ --o-visualization core-metrics-results-social-cap/unweighted-unifrac-cap-wild-significance-social-cap.qzv \ --p-pairwise # # # Social animals living in the wild: ## Calculate alpha and beta diversity metrics qiime diversity core-metrics-phylogenetic \ --i-phylogeny rooted-tree.qza \ --i-table table-social-wild.qza \ --p-sampling-depth 31265 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --output-dir core-metrics-results-social-wild # ## Calculate alpha-group-significance ### Faith's phylogenetic diversity qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-social-wild/faith_pd_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-social-wild/faith-pd-group-significance-social-wild.qzv # ### Evenness qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-social-wild/evenness_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-social-wild/evenness-group-significance-social-wild.qzv # ## Calculate beta-group-significance on the SocialGrpSizeCat metadata column qiime diversity beta-group-significance \ --i-distance-matrix core-metrics-results-social-wild/unweighted_unifrac_distance_matrix.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --m-metadata-column SocialGrpSizeCat \ --o-visualization core-metrics-results-social-wild/unweighted-unifrac-cap-wild-significance-social-wild.qzv \ --p-pairwise # # # # ---------------------------------------------------- # Experiment: DLTY4721-035 # Date: 20-Mar-2022 # # # Filter table-social to include only samples with a record for SocialGrpSize qiime feature-table filter-samples \ --i-table table-social.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --p-where "[SocialGrpSizeCat] IN ('small', 'medium', 'large')" \ --o-filtered-table table-social-na-rm.qza # # # Filter table to include only social animals that live in captivity qiime feature-table filter-samples \ --i-table table-social-na-rm.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --p-where "[captive_wild] = 'captive'" \ --o-filtered-table table-social-cap-na-rm.qza # # # Filter table to include only social animals that live in the wild qiime feature-table filter-samples \ --i-table table-social-na-rm.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --p-where "[captive_wild] = 'wild'" \ --o-filtered-table table-social-wild-na-rm.qza # # # # Visualize ASVs stats for each subsetted table # social-na-rm qiime feature-table summarize \ --i-table table-social-na-rm.qza \ --o-visualization table-social-na-rm.qzv \ --m-sample-metadata-file /root/data/project_2/zoo_metadata_mod.tsv # # social captive qiime feature-table summarize \ --i-table table-social-cap-na-rm.qza \ --o-visualization table-social-cap-na-rm.qzv \ --m-sample-metadata-file /root/data/project_2/zoo_metadata_mod.tsv # # social wild qiime feature-table summarize \ --i-table table-social-wild-na-rm.qza \ --o-visualization table-social-wild-na-rm.qzv \ --m-sample-metadata-file /root/data/project_2/zoo_metadata_mod.tsv # # #---------------------- # Diversity metrics: # Generate alpha-rarefaction curve using the max sampling depth for each table # table-no-mitochondria-no-chloroplast.qza qiime diversity alpha-rarefaction \ --i-table table-no-mitochondria-no-chloroplast.qza \ --i-phylogeny rooted-tree.qza \ --p-max-depth 236017 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization alpha-rarefaction-social-vs-non-social.qzv # # table-social-na-rm qiime diversity alpha-rarefaction \ --i-table table-social-na-rm.qza \ --i-phylogeny rooted-tree.qza \ --p-max-depth 236017 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization alpha-rarefaction-social-na-rm.qzv # # table-social-cap-na-rm qiime diversity alpha-rarefaction \ --i-table table-social-cap-na-rm.qza \ --i-phylogeny rooted-tree.qza \ --p-max-depth 236017 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization alpha-rarefaction-social-cap-na-rm.qzv # # table-social-wild-na-rm qiime diversity alpha-rarefaction \ --i-table table-social-wild-na-rm.qza \ --i-phylogeny rooted-tree.qza \ --p-max-depth 215988 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization alpha-rarefaction-social-wild-na-rm.qzv # # #---------- # Core diversty metrics generation # # Social vs. Non-social animals: ## Calculate alpha and beta diversity metrics qiime diversity core-metrics-phylogenetic \ --i-phylogeny rooted-tree.qza \ --i-table table-no-mitochondria-no-chloroplast.qza \ --p-sampling-depth 87442 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --output-dir core-metrics-results-social-vs-non-social # ## Calculate alpha-group-significance ### Faith's phylogenetic diversity qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-social-vs-non-social/faith_pd_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-social-vs-non-social/faith-pd-group-significance-social-vs-non-social.qzv # ### Evenness qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-social-vs-non-social/evenness_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-social-vs-non-social/evenness-group-significance-social-vs-non-social.qzv # ## Calculate beta-group-significance on the SocialityHMC metadata column qiime diversity beta-group-significance \ --i-distance-matrix core-metrics-results-social-vs-non-social/unweighted_unifrac_distance_matrix.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --m-metadata-column SocialityHMC \ --o-visualization core-metrics-results-social-vs-non-social/unweighted-unifrac-sociality-significance.qzv \ --p-pairwise # # # Social animals living in captivity: ## Calculate alpha and beta diversity metrics qiime diversity core-metrics-phylogenetic \ --i-phylogeny rooted-tree.qza \ --i-table table-social-cap-na-rm.qza \ --p-sampling-depth 98425 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --output-dir core-metrics-results-social-cap-na-rm # ## Calculate alpha-group-significance ### Faith's phylogenetic diversity qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-social-cap-na-rm/faith_pd_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-social-cap-na-rm/faith-pd-group-significance-social-cap-na-rm.qzv # ### Evenness qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-social-cap-na-rm/evenness_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-social-cap-na-rm/evenness-group-significance-social-cap-na-rm.qzv # ## Calculate beta-group-significance on the SocialGrpSizeCat metadata column qiime diversity beta-group-significance \ --i-distance-matrix core-metrics-results-social-cap-na-rm/unweighted_unifrac_distance_matrix.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --m-metadata-column SocialGrpSizeCat \ --o-visualization core-metrics-results-social-cap-na-rm/unweighted-unifrac-cap-wild-significance-social-cap-na-rm.qzv \ --p-pairwise # # # Social animals living in the wild: ## Calculate alpha and beta diversity metrics qiime diversity core-metrics-phylogenetic \ --i-phylogeny rooted-tree.qza \ --i-table table-social-wild-na-rm.qza \ --p-sampling-depth 30307 \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --output-dir core-metrics-results-social-wild-na-rm # ## Calculate alpha-group-significance ### Faith's phylogenetic diversity qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-social-wild-na-rm/faith_pd_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-social-wild-na-rm/faith-pd-group-significance-social-wild-na-rm.qzv # ### Evenness qiime diversity alpha-group-significance \ --i-alpha-diversity core-metrics-results-social-wild-na-rm/evenness_vector.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --o-visualization core-metrics-results-social-wild-na-rm/evenness-group-significance-social-wild-na-rm.qzv # ## Calculate beta-group-significance on the SocialGrpSizeCat metadata column qiime diversity beta-group-significance \ --i-distance-matrix core-metrics-results-social-wild-na-rm/unweighted_unifrac_distance_matrix.qza \ --m-metadata-file /root/data/project_2/zoo_metadata_mod.tsv \ --m-metadata-column SocialGrpSizeCat \ --o-visualization core-metrics-results-social-wild-na-rm/unweighted-unifrac-cap-wild-significance-social-wild-na-rm.qzv \ --p-pairwise #