parallel_alpha_diversity.py – Parallel alpha diversity

Description:

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

Usage: parallel_alpha_diversity.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_path

Input path, must be directory [REQUIRED]

-o, --output_path

Output path, must be directory [REQUIRED]

[OPTIONAL]

-t, --tree_path

Path to newick tree file, required for phylogenetic metrics [default: None]

-m, --metrics

Metrics to use, comma delimited

-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: start_parallel_jobs.py]

-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: 2]

Output:

The resulting output will be the same number of files as supplied by the user. The resulting files are tab-delimited text files, where the columns correspond to alpha diversity metrics and the rows correspond to samples and their calculated diversity measurements.

Example:

Apply the observed_species, chao1, PD_whole_tree metrics (-m) to all otu tables in rarefied_otu_tables/ (-i) and write the resulting output files to adiv/ (-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/).

parallel_alpha_diversity.py -i $PWD/rarefied_otu_tables -o $PWD/adiv -m observed_species,chao1,PD_whole_tree -t $PWD/rep_set.tre