News and Announcements » – Parallel taxonomy assignment using RDP


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

Usage: [options]

Input Arguments:



-i, --input_fasta_fp
Full path to input_fasta_fp [REQUIRED]
-o, --output_dir
Path to store output files [REQUIRED]


Full path to rdp classifier jar file [default: /Users/caporaso/Dropbox/bin/rdp_classifier_2.2/rdp_classifier-2.2.jar]
-c, --confidence
Minimum confidence to record an assignment [default: 0.5]
-t, --id_to_taxonomy_fp
Full path to id_to_taxonomy mapping file [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt]
-r, --reference_seqs_fp
Ref seqs to rdp against. [default: /Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta]
Maximum memory allocation, in MB, for Java virtual machine when using the rdp method. Increase for large training sets [default: 4000]
-O, --jobs_to_start
Number of jobs to start [default: 1]
-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:]
-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]


Mapping of sequence identifiers to taxonomy and quality scores.


Assign taxonomy to all sequences in the input file (-i) using the RDP classifier and write the results (-o) to $PWD/rdp_assigned_taxonomy/. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/). -i $PWD/inseqs.fasta -o $PWD/rdp_assigned_taxonomy/