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.. _parallel_blast:
.. index:: parallel_blast.py
*parallel_blast.py* -- Parallel BLAST
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
This script for performing blast while making use of multicore/multiprocessor environments to perform analyses in parallel.
**Usage:** :file:`parallel_blast.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-infile_path
Path of sequences to use as queries [REQUIRED]
-r, `-`-refseqs_path
Path to fasta sequences to search against [REQUIRED]
-o, `-`-output_dir
Name of output directory for blast jobs [REQUIRED]
**[OPTIONAL]**
-c, `-`-disable_low_complexity_filter
Disable filtering of low-complexity sequences (i.e., -F F is passed to blast) [default: False]
-e, `-`-e_value
E-value threshold for blasts [default: 1e-30]
-n, `-`-num_hits
Number of hits per query for blast results [default: 1]
-w, `-`-word_size
Word size for blast searches [default: 30]
-D, `-`-suppress_format_blastdb
Supress format of blastdb [default: False]
-a, `-`-blastmat_dir
Full path to directory containing blastmat file [default: /software/blast-2.2.22/data]
-b, `-`-blastall_fp
Path to blastall [default: blastall]
-O, `-`-jobs_to_start
Number of jobs to start [default: 1]
-P, `-`-poller_fp
Full path to qiime/parallel/`poller.py <./poller.html>`_ [default: /Users/jistombaugh/Dropbox/Qiime_work/scripts/`poller.py <./poller.html>`_]
-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: /Users/jistombaugh/Dropbox/Qiime_work/scripts/`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]
-Y, `-`-python_exe_fp
Full path to python executable [default: /Library/Frameworks/Python.framework/Versions/2.7/bin/python]
-Z, `-`-seconds_to_sleep
Number of seconds to sleep between checks for run completion when polling runs [default: 60]
**Output:**
**Example:**
BLAST /home/qiime_user/10_seq.fasta (-i) via three (-O) independent jobs against a blast database created from /home/qiime_user/1000_seq.fasta (-r). Store the results in /home/qiime_user/bla_out/ (-o).
::
parallel_blast.py -i /home/qiime_user/10_seq.fasta -r /home/qiime_user/1000_seq.fasta -O 3 -o /home/qiime_user/bla_out/
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