QIIME2

Overview

QIIME2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed, see https://qiime2.org/

Set up procedure

Central install

To use the install already available, see below.
Do -not- run any heavy lifting on the login nodes, instead submit a batch job.

2021.11

module load apps/anaconda3/5.2.0/bin
source /opt/apps/apps/python/conda_init/conda_init_bash.sh
conda activate /opt/apps/apps/python/qiime2/2021.11
qiime info

2021.4

module load apps/anaconda3/5.2.0/bin
source /opt/apps/apps/python/conda_init/conda_init_bash.sh
conda activate /opt/apps/apps/python/qiime2/2021.4
qiime info

As a central install, users cannot write to the QIIME2 conda environment (if they wanted to add their own packages).

There is an older version of QIIME2, also available:

module load apps/qiime2/2019.1.0/bin

Local install

If you’d like to install your own version that you can modify, you can run:

qrsh -l short
module load apps/python/miniconda3/4.10.3
conda config --set auto_activate_base false
module load tools/env/proxy
wget https://data.qiime2.org/distro/core/qiime2-2022.8-py38-linux-conda.yml
http_proxy=http://proxy.man.ac.uk:3128
https_proxy=http://proxy.man.ac.uk:3128
mkdir -p /scratch/$USER/qiime2/2022.8
conda env create --prefix=/scratch/$USER/qiime2/2022.8 --file qiime2-2022.8-py38-linux-conda.yml # takes ~1 hour 
rm qiime2-2022.8-py38-linux-conda.yml # optional cleanup
conda activate qiime2-2022.8 
qiime info

You’ll just need this bit to use your personal qiime2 install in a jobscript in the future:

module load apps/anaconda3/5.2.0/bin
source /opt/apps/apps/python/conda_init/conda_init_bash.sh
conda activate qiime2-2022.8

Example parallel job

Here is an 8 core job, using a central install as an example:

#!/bin/bash --login
#$ -cwd              # Job will run from the current directory
#$ -pe smp.pe 8      # Number of cores (can be 2--24)
#$ -N ASV-DADA2  # Give the job a name

# Input 1: single end Illumina sequences (.fastq)
# Input 2: Manifest file (sequences.tsv) validated with keemei 

module load apps/anaconda3/5.2.0/bin 
source /opt/apps/apps/python/conda_init/conda_init_bash.sh 
conda activate /opt/apps/apps/python/qiime2/2021.4

# Import sequences

qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path sequences.tsv --output-path sequences.qza  --input-format SingleEndFastqManifestPhred33V2

# Denoise with DADA2

qiime dada2 denoise-single --i-demultiplexed-seqs sequences.qza --p-trim-left 0 --p-trunc-len 251 --o-representative-sequences rep-seqs.qza --o-table table.qza --o-denoising-stats stats-dada2.qza
qiime feature-table summarize --i-table table.qza --o-visualization table.qzv
qiime metadata tabulate --m-input-file stats-dada2.qza --o-visualization stats-dada2.qzv
qiime feature-table tabulate-seqs --i-data rep-seqs.qza --o-visualization rep-seqs.qzv

# Taxnomic asignation
qiime feature-classifier classify-sklearn --i-classifier silva-138-99-nb-classifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
qiime metadata tabulate --m-input-file taxonomy.qza  --o-visualization taxonomy.qzv
qiime taxa barplot --i-table table.qza --i-taxonomy taxonomy.qza --m-metadata-file metadata.tsv --o-visualization taxa-bar-plots.qzv