parallel_assign_taxonomy_rdp.py – Parallel taxonomy assignment using RDP

Description:

This script performs like the assign_taxonomy.py script, but is intended to make use of multicore/multiprocessor environments to perform analyses in parallel.

Usage: parallel_assign_taxonomy_rdp.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fasta_fp

Full path to input_fasta_fp [REQUIRED]

-o, --output_dir

Path to store output files [REQUIRED]

[OPTIONAL]

--rdp_classifier_fp

Full path to rdp classifier jar file [default: /software/rdp_classifier/rdp_classifier-2.2.jar]

-c, --confidence

Minimum confidence to record an assignment [default: 0.8]

-N, --assign_taxonomy_fp

Full path to scripts/assign_taxonomy.py [default: /Users/jistombaugh/Dropbox/Qiime_work/scripts/assign_taxonomy.py]

-t, --id_to_taxonomy_fp

Full path to id_to_taxonomy mapping file [default: /software/greengenes_tax_rdp_train.txt]

-r, --reference_seqs_fp

Ref seqs to rdp against. [default: /software/gg_97_otus_4feb2011.fasta]

--rdp_max_memory

Maximum memory allocation, in MB, for Java virtual machine when using the rdp method. Increase for large training sets [default: 1000]

-O, --jobs_to_start

Number of jobs to start [default: 1]

-P, --poller_fp

Full path to qiime/parallel/poller.py [default: /Users/jistombaugh/Dropbox/Qiime_work/scripts/poller.py]

-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: /Users/jistombaugh/Dropbox/Qiime_work/scripts/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]

-Y, --python_exe_fp

Full path to python executable [default: /Library/Frameworks/Python.framework/Versions/2.7/bin/python]

-Z, --seconds_to_sleep

Number of seconds to sleep between checks for run completion when polling runs [default: 60]

Output:

Mapping of sequence identifiers to taxonomy and quality scores.

Example:

Assign taxonomy to all sequences in the input file (-i) via five (-O) independent jobs using the RDP classifier and write the results (-o) to /home/qiime_user/out/.

parallel_assign_taxonomy_rdp.py -O 5 -i /home/qiime_user/inseqs.fasta -o /home/qiime_user/out/