News and Announcements » – Parallel pick otus using SortMeRNA


This script works 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
Path to input fasta file.
-o, --output_dir
Directory where output should be written.
-r, --refseqs_fp
Path to reference fasta file.


-s, --similarity
Sequence similarity threshold [default: 0.97]
Pre-existing database to search against when using -m sortmerna [default: None]
Maximum E-value when clustering [default = 1]
Mininum percent query coverage (of an alignment) to consider a hit, expressed as a fraction between 0 and 1 [default: 0.97]
Output alignments in the Blast-like tabular format with two additional columns including the CIGAR string and the percent query coverage [default: False]
Must be set together with –sortmerna_tabular. This option specifies how many alignments per read will be written [default: 1]
The maximum number of positions per seed to store in the indexed database [default: 10000]
Specify the number of threads to use per job. Use –jobs_to_start to specify the number of jobs.[default: 1]
-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]


The output consists of two files (i.e. seqs_otus.txt and seqs_otus.log). The .txt file is composed of tab-delimited lines, where the first field on each line corresponds to an OTU identifier which is the reference sequence identifier, and the remaining fields correspond to sequence identifiers assigned to that OTU. The resulting .log file contains a list of parameters passed to this script along with the output location of the resulting .txt file.


Pick OTUs by searching $PWD/inseqs.fasta against $PWD/refseqs.fasta with reference-based sortmerna and write the output to the $PWD/smr_otus/ directory. This is a closed-reference OTU picking process. ALWAYS SPECIFY ABSOLUTE FILE PATHS (absolute path represented here as $PWD, but will generally look something like /home/ubuntu/my_analysis/). -i $PWD/seqs.fna -r $PWD/refseqs.fna -o $PWD/smr_otus/