parallel_blast.py – Parallel BLAST

Description:

This script for performing blast while making use of multicore/multiprocessor environments to perform analyses in parallel.

Usage: 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 [default: /Users/jistombaugh/Dropbox/Qiime_work/scripts/poller.py]

-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]

-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/