parallel_map_reads_to_reference.py –

Description:

Usage: parallel_map_reads_to_reference.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_seqs_filepath

Path to input sequences file

-o, --output_dir

Directory to store results

-r, --refseqs_fp

Path to reference sequences

[OPTIONAL]

-t, --observation_metadata_fp

Path to observation metadata (e.g., taxonomy, EC, etc) [default: None]

-m, --assignment_method

Method for picking OTUs. Valid choices are: usearch blat bwa-short. [default: usearch]

-e, --evalue

Max e-value to consider a match [default: 1e-10]

-s, --min_percent_id

Min percent id to consider a match [default: 0.75]

--max_diff

MaxDiff to consider a match (applicable for -m bwa) – see the aln section of “man bwa” for details [default (defined by bwa): 0.04]

--queryalnfract

Min percent of the query seq that must match to consider a match (usearch only) [default: 0.35]

--targetalnfract

Min percent of the target/reference seq that must match to consider a match (usearch only) [default: 0.0]

--max_accepts

Max_accepts value (usearch only) [default: 1]

--max_rejects

Max_rejects value to (usearch only) [default: 32]

-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:

parallel_map_reads_to_reference.py -i $PWD/query_nt.fasta -r $PWD/refseqs_pr.fasta -o $PWD/usearch_mapped

parallel_map_reads_to_reference.py -i $PWD/query_nt.fasta -r $PWD/refseqs_pr.fasta -o $PWD/blat_mapped -m blat

parallel_map_reads_to_reference.py -i $PWD/query_nt.fasta -r $PWD/refseqs_nt.fasta -o $PWD/bwa-short_mapped -m bwa-short