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.. _parallel_pick_otus_uclust_ref:
.. index:: parallel_pick_otus_uclust_ref.py
*parallel_pick_otus_uclust_ref.py* -- Parallel pick otus using uclust_ref
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
This script works like the `pick_otus.py <./pick_otus.html>`_ script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel.
**Usage:** :file:`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 <./start_parallel_jobs.html>`_]
-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/
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