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