QiimeClosedRefClassifier#

Add to module run order:
#BioModule biolockj.module.classifier.r16s.QiimeClosedRefClassifier

Description#

Pick OTUs using a closed reference database and construct an OTU table via the QIIME script pick_closed_reference_otus.py

Properties#

Properties are the name=value pairs in the configuration file.

QiimeClosedRefClassifier properties:#

Property	Description
exe.vsearch	executable Path for the "vsearch" executable; if not supplied, any script that needs the vsearch command will assume it is on the PATH. default: null
qiime.params	list Parameters for qiime default: null
qiime.pynastAlignDB	file path path to define ~/.qiime_config pynast_template_alignment_fp default: null
qiime.refSeqDB	file path path to define ~/.qiime_config pick_otus_reference_seqs_fp and assign_taxonomy_reference_seqs_fp default: null
qiime.removeChimeras	boolean if vsearch is needed for chimera removal default: Y
qiime.taxaDB	file path path to define ~/.qiime_config assign_taxonomy_id_to_taxonomy_fp default: null
qiime.vsearchParams	list Parameters for vsearch default: null

General properties applicable to this module:#

Property	Description
cluster.batchCommand	string Terminal command used to submit jobs on the cluster default: null
cluster.jobHeader	string Header written at top of worker scripts default: null
cluster.modules	list List of cluster modules to load at start of worker scripts default: null
cluster.prologue	string To run at the start of every script after loading cluster modules (if any) default: null
cluster.statusCommand	string Terminal command used to check the status of jobs on the cluster default: null
docker.saveContainerOnExit	boolean If Y, docker run command will NOT include the --rm flag default: null
docker.verifyImage	boolean In check dependencies, run a test to verify the docker image. default: null
exe.awk	executable Path for the "awk" executable; if not supplied, any script that needs the awk command will assume it is on the PATH. default: null
pipeline.defaultFastaConverter	string Java class name for default module used to convert files into fasta format default: biolockj.module.seq.AwkFastaConverter
pipeline.defaultSeqMerger	string Java class name for default module used combined paired read files default: biolockj.module.seq.PearMergeReads
script.defaultHeader	string Store default script header for MAIN script and locally run WORKER scripts. default: #!/bin/bash
script.numThreads	integer Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter. default: 8
script.numWorkers	integer Set number of samples to process per script (if parallel processing) default: 1
script.permissions	string Used as chmod permission parameter (ex: 774) default: 770
script.timeout	integer Sets # of minutes before worker scripts times out. default: null

Details#

version: 0.0.0 This module picks OTUs using a closed reference database and constructs an OTU table via the QIIME script pick_closed_reference_otus.py. Taxonomy is assigned using a pre-defined taxonomy map of reference sequence OTU to taxonomy. This is the fastest OTU picking method since samples can be processed in parallel batches. Before the QIIME script is run, batches are prepared in the temp directory, with each batch directory containing a fasta directory with script.batchSize fasta files and a QIIME mapping file, created with awk, called batchMapping.tsv for the batch of samples. Inherits from QiimeClassifier.

Adds modules#

pre-requisite modules
pipeline-dependent
post-requisite modules
biolockj.module.implicit.qiime.QiimeClassifier
biolockj.module.implicit.parser.r16s.QiimeParser

Docker#

If running in docker, this module will run in a docker container from this image:

biolockjdevteam/qimme_classifier:v1.1

This can be modified using the following properties:
QiimeClosedRefClassifier.imageOwner
QiimeClosedRefClassifier.imageName
QiimeClosedRefClassifier.imageTag

Citation#

QIIME allows analysis of high-throughput community sequencing data
J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Pena, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld and Rob Knight; Nature Methods, 2010; doi:10.1038/nmeth.f.303
(needs further citation)
http://www.wernerlab.org/software/macqiime/citations