News and Announcements » – Parallel alpha 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]


-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:]
-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]


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.


Apply the observed_OTUs, 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/). -i $PWD/rarefied_otu_tables -o $PWD/adiv -m observed_otus,chao1,PD_whole_tree -t $PWD/rep_set.tre