News and Announcements » – Parallel pick otus using BLAST


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

Usage: [options]

Input Arguments:



-i, --input_fasta_fp
Full path to input_fasta_fp
-o, --output_dir
Path to store output files


-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]
Minimum percent of query sequence that can be aligned to consider a hit, expressed as a fraction between 0 and 1 (BLAST OTU picker only) [default: 0.5]
-O, --jobs_to_start
Number of jobs to start [default: 1]
-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:]
-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]


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.


Pick OTUs by blasting $PWD/inseqs.fasta against $PWD/refseqs.fasta and write the output to the $PWD/blast_otus/ directory. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/). -i $PWD/seqs.fna -r $PWD/refseqs.fna -o $PWD/blast_otus/