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.. _parallel_assign_taxonomy_rdp:
.. index:: parallel_assign_taxonomy_rdp.py
*parallel_assign_taxonomy_rdp.py* -- Parallel taxonomy assignment using RDP
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
This script performs like the `assign_taxonomy.py <./assign_taxonomy.html>`_ script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel.
**Usage:** :file:`parallel_assign_taxonomy_rdp.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_fasta_fp
Full path to input_fasta_fp [REQUIRED]
-o, `-`-output_dir
Path to store output files [REQUIRED]
**[OPTIONAL]**
`-`-rdp_classifier_fp
Full path to rdp classifier jar file [default: /Applications/rdp_classifier_2.2/rdp_classifier-2.2.jar]
-c, `-`-confidence
Minimum confidence to record an assignment [default: 0.8]
-t, `-`-id_to_taxonomy_fp
Full path to id_to_taxonomy mapping file [default: /Users/caporaso/data/gg_13_5_otus/taxonomy/97_otu_taxonomy.txt]
-r, `-`-reference_seqs_fp
Ref seqs to rdp against. [default: /Users/caporaso/data/gg_13_5_otus/rep_set/97_otus.fasta]
`-`-rdp_max_memory
Maximum memory allocation, in MB, for Java virtual machine when using the rdp method. Increase for large training sets [default: 4000]
-O, `-`-jobs_to_start
Number of jobs to start [default: 2]
-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]
**Output:**
Mapping of sequence identifiers to taxonomy and quality scores.
**Example:**
Assign taxonomy to all sequences in the input file (-i) using the RDP classifier and write the results (-o) to $PWD/rdp_assigned_taxonomy/. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).
::
parallel_assign_taxonomy_rdp.py -i $PWD/inseqs.fasta -o $PWD/rdp_assigned_taxonomy/
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