parallel_pick_otus_blast.py – Parallel pick otus using BLAST

Description:

This script performs like the pick_otus.py script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel.

Usage: parallel_pick_otus_blast.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fasta_fp

Full path to input_fasta_fp

-o, --output_dir

Path to store output files

[OPTIONAL]

-e, --max_e_value

Max E-value [default: 1e-10]

-s, --similarity

Sequence similarity threshold [default: 0.97]

-r, --refseqs_fp

Full path to template alignment [default: None]

-b, --blast_db

Database to blast against [default: None]

--min_aligned_percent

Minimum percent of query sequence that can be aligned to consider a hit (BLAST OTU picker only) [default: 0.5]

-N, --pick_otus_fp

Full path to scripts/pick_otus.py [default: /Users/jistombaugh/Dropbox/Qiime_work/scripts/pick_otus.py]

-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:

The output consists of two files (i.e. seqs_otus.txt and seqs_otus.log). The .txt file is composed of tab-delimited lines, where the first field on each line corresponds to an (arbitrary) cluster identifier, and the remaining fields correspond to sequence identifiers assigned to that cluster. Sequence identifiers correspond to those provided in the input FASTA file. The resulting .log file contains a list of parameters passed to this script along with the output location of the resulting .txt file.

Example:

Pick OTUs by blasting /home/qiime_user/inseqs.fasta against /home/qiime_user/refseqs.fasta and write the output to the /home/qiime_user/out/ directory.

parallel_pick_otus_blast.py -i /home/qiime_user/inseqs.fasta -r /home/qiime_user/refseqs.fasta -o /home/qiime_user/out/