parallel_pick_otus_usearch61_ref.py – Parallel pick otus using usearch_ref

Description:

This script works 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_usearch61_ref.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fasta_fp

Full path to input_fasta_fp

-o, --output_dir

Path to store output files

-r, --refseqs_fp

Full path to reference collection

[OPTIONAL]

-s, --similarity

Sequence similarity threshold [default: 0.97]

-z, --enable_rev_strand_match

Enable reverse strand matching for uclust, uclust_ref, usearch, usearch_ref, usearch61, or usearch61_ref otu picking, will double the amount of memory used. [default: False]

--max_accepts

Max_accepts value to uclust, uclust_ref, usearch61, and usearch61_ref. By default, will use value suggested by method (uclust: 20, usearch61: 1) [default: default]

--max_rejects

Max_rejects value for uclust, uclust_ref, usearch61, and usearch61_ref. With default settings, will use value recommended by clustering method used (uclust: 500, usearch61: 8 for usearch_fast_cluster option, 32 for reference and smallmem options) [default: default]

--word_length

Word length value for uclust, uclust_ref, and usearch, usearch_ref, usearch61, and usearch61_ref. With default setting, will use the setting recommended by the method (uclust: 12, usearch: 64, usearch61: 8). int value can be supplied to override this setting. [default: default]

--minlen

Minimum length of sequence allowed for usearch, usearch_ref, usearch61, and usearch61_ref. [default: 64]

--usearch_fast_cluster

Use fast clustering option for usearch or usearch61_ref with new clusters. –enable_rev_strand_match can not be enabled with this option, and the only valid option for usearch61_sort_method is ‘length’. This option uses more memory than the default option for de novo clustering. [default: False]

--usearch61_sort_method

Sorting method for usearch61 and usearch61_ref. Valid options are abundance, length, or None. If the –usearch_fast_cluster option is enabled, the only sorting method allowed in length. [default: abundance]

--sizeorder

Enable size based preference in clustering with usearch61. Requires that –usearch61_sort_method be abundance. [default: False]

-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: 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]

-Z, --seconds_to_sleep

Number of seconds to sleep between checks for run completion when polling runs [default: 1]

Output:

Example:

Pick OTUs by searching $PWD/inseqs.fasta against $PWD/refseqs.fasta with reference-based usearch and write the output to the $PWD/usearch_ref_otus/ directory. This is a closed-reference OTU picking process. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/).

parallel_pick_otus_usearch61_ref.py -i $PWD/seqs.fna -r $PWD/refseqs.fna -o $PWD/usearch_ref_otus/