News and Announcements » – Parallel beta diversity


This script performs like the script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel.

Usage: [options]

Input Arguments:



-i, --input_path
Input path, must be directory [REQUIRED]
-o, --output_path
Output path, must be directory [REQUIRED]


-m, --metrics
Beta-diversity metric(s) to use. A comma-separated list should be provided when multiple metrics are specified. [default: unweighted_unifrac,weighted_unifrac]
-t, --tree_path
Path to newick tree file, required for phylogenetic metrics [default: None]
-R, --retain_temp_files
Retain temporary files after runs complete (useful for debugging) [default: False]
-S, --suppress_submit_jobs
Only split input and write commands file - don’t submit jobs [default: False]
-T, --poll_directly
Poll directly for job completion rather than running poller as a separate job. If -T is specified this script will not return until all jobs have completed. [default: False]
-U, --cluster_jobs_fp
Path to cluster jobs script (defined in qiime_config) [default:]
-W, --suppress_polling
Suppress polling of jobs and merging of results upon completion [default: False]
-X, --job_prefix
Job prefix [default: descriptive prefix + random chars]
-Z, --seconds_to_sleep
Number of seconds to sleep between checks for run completion when polling runs [default: 1]
-O, --jobs_to_start
Number of jobs to start [default: 1]
-f, --full_tree
By default, each job removes calls _fast_unifrac_setup to remove unused parts of the tree. pass -f if you already have a minimal tree, and this script will run faster


The output of is a folder containing text files, each a distance matrix between samples.

Apply in parallel to multiple otu tables:

Apply the unweighted_unifrac and weighted_unifrac metrics (modify with -m) to all otu tables in rarefied_otu_tables (-i) and write the resulting output files to bdiv/ (-o, will be created if it doesn’t exist). Use the rep_set.tre (-t) to compute phylogenetic diversity metrics. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/). -i $PWD/rarefied_otu_tables/ -o $PWD/bdiv/ -t $PWD/rep_set.tre

Apply in parallel to a single otu table: -i $PWD/otu_table.biom -o $PWD/bdiv_single/ -t $PWD/rep_set.tre