.. _pick_subsampled_reference_otus_through_otu_table:

.. index:: pick_subsampled_reference_otus_through_otu_table.py

*pick_subsampled_reference_otus_through_otu_table.py* -- 
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**Description:**




**Usage:** :file:`pick_subsampled_reference_otus_through_otu_table.py [options]`

**Input Arguments:**

.. note::

	
	**[REQUIRED]**
		
	-i, `-`-input_fps
		The input sequences filepath or comma-separated list of filepaths
	-r, `-`-reference_fp
		The reference sequences
	-o, `-`-output_dir
		The output directory
	
	**[OPTIONAL]**
		
	-p, `-`-parameter_fp
		Path to the parameter file, which specifies changes to the default behavior. See http://www.qiime.org/documentation/file_formats.html#qiime-parameters . [if omitted, default values will be used]
	-n, `-`-new_ref_set_id
		Unique identifier for OTUs that get created in this ref set (this is useful to support combining of reference sets) [default:New]
	-f, `-`-force
		Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: None]
	-a, `-`-parallel
		Run in parallel where available [default: False]
	-O, `-`-jobs_to_start
		Number of jobs to start. NOTE: you must also pass -a to run in parallel, this defines the number of jobs to be started if and only if -a is passed [default: 2]
	-s, `-`-percent_subsample
		Percent of failure sequences to include in the subsample to cluster de novo (larger numbers should give more comprehensive ,results but will be slower) [default:0.001]
	`-`-prefilter_percent_id
		Sequences are pre-clustered at this percent id against the reference and any reads which fail to hit are discarded (a quality filter); pass 0.0 to disable [default:0.60]
	`-`-step1_otu_map_fp
		Reference OTU picking OTU map  (to avoid rebuilding if one has already been built)
	`-`-step1_failures_fasta_fp
		Reference OTU picking failures fasta filepath  (to avoid rebuilding if one has already been built)
	`-`-suppress_step4
		Suppress the final de novo OTU picking step  (may be necessary for extremely large data sets) [default: False]
	`-`-min_otu_size
		The minimum otu size (in number of sequences) to retain the otu [default: 2]


**Output:**




Run the subsampled open-reference OTU picking workflow on seqs1.fna using refseqs.fna as the reference collection. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/

::

	pick_subsampled_reference_otus_through_otu_table.py -i $PWD/seqs1.fna -r $PWD/refseqs.fna -o $PWD/ucrss/ -s 0.1 -p $PWD/ucrss_params.txt

Run the subsampled open-reference OTU picking workflow in iterative mode on seqs1.fna and seqs2.fna using refseqs.fna as the initial reference collection. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/

::

	pick_subsampled_reference_otus_through_otu_table.py -i $PWD/seqs1.fna,$PWD/seqs2.fna -r $PWD/refseqs.fna -o $PWD/ucrss_iter/ -s 0.1 -p $PWD/ucrss_params.txt


