QiimeOpenRefClassifier#

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

Description#

Run the QIIME pick_open_reference_otus.py script on all fasta sequence files

Properties#

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

QiimeOpenRefClassifier 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
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 runs the QIIME pick_open_reference_otus.py script on all fasta sequence files in a single script since clusters not identified in the reference database are assigned by a clustering algorithm. Additional parameters for this script are set using exe.classifierParams. If qiime.removeChimeras = "Y", vsearch is used to find chimeric sequences in the output and the QIIME script filter_otus_from_otu_table.py is run to remove them from ./output/otu_table.biom. 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:
QiimeOpenRefClassifier.imageOwner
QiimeOpenRefClassifier.imageName
QiimeOpenRefClassifier.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