QIIME2-Sapelo2
Category
Bioinformatics
Program On
Sapelo2
Version
2019.10, 2020.2, 2020.6, 2020.11
Author / Distributor
Description
QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed."
More details are at QIIME2
Running Program
Also refer to Running Jobs on Sapelo2
- Version 2019.10 installed as a conda environment at /apps/eb/QIIME2/2019.10
- Version 2020.2 installed as a conda environment at /apps/eb/QIIME2/2020.2
- Version 2020.6 installed as a conda environment at /apps/eb/QIIME2/2020.6
- Version 2020.11 installed as a conda environment at /apps/eb/QIIME2/2020.11
To use version 2019.10, please first load the module with
module load QIIME2/2019.10
To use version 2020.2, please first load the module with
module load QIIME2/2020.2
To use version 2020.6, please first load the module with
module load QIIME2/2020.6
To use version 2020.11, please first load the module with
module load QIIME2/2020.11
Example of a shell script sub.sh to run QIIME2 2020.11 at the batch queue:
#!/bin/bash #SBATCH --job-name=j_qiime2 # Job name #SBATCH --partition=batch # Partition (queue) name #SBATCH --ntasks=1 # Run on a single CPU by default #SBATCH --cpus-per-task=1 # Number of CPU cores per task #SBATCH --mem=20gb # Job memory request #SBATCH --time=48:00:00 # Time limit hrs:min:sec #SBATCH --output=log.%j.out # Standard output log #SBATCH --error=log.%j.err # Standard error log #SBATCH --mail-type=ALL # Mail events (NONE, BEGIN, END, FAIL, ALL) #SBATCH --mail-user=username@uga.edu # Where to send mail cd $SLURM_SUBMIT_DIR ml QIIME2/2020.11 echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc qiime [OPTIONS] COMMAND [ARGS]...
where [OPTIONS], COMMAND, and [ARGS] need to be replaced by the options, command, and arguments you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number cores per node, and the job name need to be modified appropriately as well.
Example of job submission
sbatch ./sub.sh
Documentation
ml QIIME2/2020.11
qiime --help
Usage: qiime [OPTIONS] COMMAND [ARGS]...
QIIME 2 command-line interface (q2cli)
--------------------------------------
To get help with QIIME 2, visit https://qiime2.org.
To enable tab completion in Bash, run the following command or add it to
your .bashrc/.bash_profile:
source tab-qiime
To enable tab completion in ZSH, run the following commands or add them to
your .zshrc:
autoload bashcompinit && bashcompinit && source tab-qiime
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
info Display information about current deployment.
tools Tools for working with QIIME 2 files.
dev Utilities for developers and advanced users.
alignment Plugin for generating and manipulating alignments.
composition Plugin for compositional data analysis.
cutadapt Plugin for removing adapter sequences, primers, and
other unwanted sequence from sequence data.
dada2 Plugin for sequence quality control with DADA2.
deblur Plugin for sequence quality control with Deblur.
demux Plugin for demultiplexing & viewing sequence quality.
diversity Plugin for exploring community diversity.
diversity-lib Plugin for computing community diversity.
emperor Plugin for ordination plotting with Emperor.
feature-classifier Plugin for taxonomic classification.
feature-table Plugin for working with sample by feature tables.
fragment-insertion Plugin for extending phylogenies.
gneiss Plugin for building compositional models.
longitudinal Plugin for paired sample and time series analyses.
metadata Plugin for working with Metadata.
phylogeny Plugin for generating and manipulating phylogenies.
quality-control Plugin for quality control of feature and sequence data.
quality-filter Plugin for PHRED-based filtering and trimming.
sample-classifier Plugin for machine learning prediction of sample
metadata.
taxa Plugin for working with feature taxonomy annotations.
vsearch Plugin for clustering and dereplicating with vsearch.
Installation
source code from QIIME2
System
64-bit Linux