parallel_pick_otus_sortmerna.py – Parallel pick otus using SortMeRNA

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_sortmerna.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fasta_fp

Path to input fasta file.

-o, --output_dir

Directory where output should be written.

-r, --refseqs_fp

Path to reference fasta file.

[OPTIONAL]

-s, --similarity

Sequence similarity threshold [default: 0.97]

--sortmerna_db

Pre-existing database to search against when using -m sortmerna [default: None]

--sortmerna_e_value

Maximum E-value when clustering [default = 1]

--sortmerna_coverage

Mininum percent query coverage (of an alignment) to consider a hit, expressed as a fraction between 0 and 1 [default: 0.97]

--sortmerna_tabular

Output alignments in the Blast-like tabular format with two additional columns including the CIGAR string and the percent query coverage [default: False]

--sortmerna_best_N_alignments

Must be set together with –sortmerna_tabular. This option specifies how many alignments per read will be written [default: 1]

--sortmerna_max_pos

The maximum number of positions per seed to store in the indexed database [default: 10000]

--threads

Specify the number of threads to use per job. Use –jobs_to_start to specify the number of jobs.[default: 1]

-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:

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 sortmerna and write the output to the $PWD/smr_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_sortmerna.py -i $PWD/seqs.fna -r $PWD/refseqs.fna -o $PWD/smr_otus/