parallel_pick_otus_uclust_ref.py – Parallel pick otus using uclust_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_uclust_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 otu picking, will double the amount of memory used. [default: False]

-A, --optimal_uclust

Pass the –optimal flag to uclust for uclust otu picking. [default: False]

-E, --exact_uclust

Pass the –exact flag to uclust for uclust otu picking. [default: False]

--max_accepts

Max_accepts value to uclust and uclust_ref [default: 20]

--max_rejects

Max_rejects value to uclust and uclust_ref [default: 500]

--stepwords

Stepwords value to uclust and uclust_ref [default: 20]

--word_length

W value to uclust and uclust_ref [default: 12]

--uclust_stable_sort

Deprecated: stable sort enabled by default, pass –uclust_suppress_stable_sort to disable [default: True]

--suppress_uclust_stable_sort

Don’t pass –stable-sort to uclust [default: False]

-d, --save_uc_files

Enable preservation of intermediate uclust (.uc) files that are used to generate clusters via uclust. [default: True]

--uclust_otu_id_prefix

OTU identifier prefix (string) for the de novo uclust OTU picker [default: None, OTU ids are ascending integers]

-O, --jobs_to_start

Number of jobs to start [default: 2]

-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:

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 OTU identifier which is the reference sequence identifier, and the remaining fields correspond to sequence identifiers assigned to that OTU. 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 searching $PWD/inseqs.fasta against $PWD/refseqs.fasta with reference-based uclust and write the output to the $PWD/blast_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_uclust_ref.py -i $PWD/seqs.fna -r $PWD/refseqs.fna -o $PWD/ucref_otus/