pick_subsampled_reference_otus_through_otu_table.py –

Description:

Usage: 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