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.. _parallel_map_reads_to_reference:
.. index:: parallel_map_reads_to_reference.py
*parallel_map_reads_to_reference.py* --
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
**Usage:** :file:`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 <./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:**
::
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
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