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.. _parallel_multiple_rarefactions:
.. index:: parallel_multiple_rarefactions.py
*parallel_multiple_rarefactions.py* -- Parallel multiple file rarefaction
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
This script performs like the `multiple_rarefactions.py <./multiple_rarefactions.html>`_ script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel.
**Usage:** :file:`parallel_multiple_rarefactions.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_path
Input filepath, (the otu table) [REQUIRED]
-o, `-`-output_path
Write output rarefied otu tables here makes dir if it doesn't exist [REQUIRED]
-m, `-`-min
Min seqs/sample [REQUIRED]
-x, `-`-max
Max seqs/sample (inclusive) [REQUIRED]
**[OPTIONAL]**
-n, `-`-num-reps
Num iterations at each seqs/sample level [default: 10]
`-`-suppress_lineages_included
Exclude taxonomic (lineage) information for each OTU.
-s, `-`-step
Levels: min, min+step... for level <= max [default: 1]
`-`-subsample_multinomial
Subsample using subsampling with replacement [default: False]
-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 <./start_parallel_jobs.html>`_]
-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 result of `parallel_multiple_rarefactions.py <./parallel_multiple_rarefactions.html>`_ consists of a number of files, which depend on the minimum/maximum number of sequences per samples, steps and iterations. The files have the same otu table format as the input otu_table.biom, and are named in the following way: rarefaction_100_0.txt, where "100" corresponds to the sequences per sample and "0" for the iteration.
**OTU tables of different depths:**
Build rarefied otu tables containing 10 (-m) to 140 (-x) sequences in steps of 10 (-s) with 2 (-n) repetions per number of sequences, from otu_table.biom (-i). Write the output files to the rarefied_otu_tables directory (-o, will be created if it doesn't exist). The name of the output files will be of the form rarefaction_<num_seqs>_<reptition_number>.biom. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).
::
parallel_multiple_rarefactions.py -o $PWD/rarefied_otu_tables/ -m 10 -x 140 -s 10 -n 2 -i $PWD/otu_table.biom
**OTU tables of the same depth:**
Build 8 rarefied otu tables each containing exactly 100 sequences per sample (even depth rarefaction). ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).
::
parallel_multiple_rarefactions.py -o $PWD/even_otu_tables/ -m 100 -x 100 -n 8 -i $PWD/otu_table.biom
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