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.. _parallel_align_seqs_pynast:
.. index:: parallel_align_seqs_pynast.py
*parallel_align_seqs_pynast.py* -- Parallel sequence alignment using PyNAST
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
A wrapper for the `align_seqs.py <./align_seqs.html>`_ PyNAST option, intended to make use of multicore/multiprocessor environments to perform analyses in parallel.
**Usage:** :file:`parallel_align_seqs_pynast.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_fasta_fp
Path to the input fasta file
-o, `-`-output_dir
Path to the output directory
**[OPTIONAL]**
-a, `-`-pairwise_alignment_method
Method to use for pairwise alignments [default: uclust]
-d, `-`-blast_db
Database to blast against [default: created on-the-fly from template_alignment]
-e, `-`-min_length
Minimum sequence length to include in alignment [default: 75% of the median input sequence length]
-p, `-`-min_percent_id
Minimum percent sequence identity to closest blast hit to include sequence in alignment [default: 75.0]
-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]
-t, `-`-template_fp
Filepath for template against [default: /Users/caporaso/data/greengenes_core_sets/core_set_aligned_imputed.fasta_11_8_07.no_dots]
**Output:**
This results in a multiple sequence alignment (FASTA-formatted).
**Example:**
Align the input file (-i) against using PyNAST and write the output (-o) to $PWD/pynast_aligned_seqs/. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).
::
parallel_align_seqs_pynast.py -i $PWD/inseqs.fasta -o $PWD/pynast_aligned_seqs/
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