Using QIIME2 on Quest

QIIME2 (Quantitative Insights into Microbial Ecology version 2) is an open-source computing platform for processing and analyzing amplicon DNA sequence data. This page describes how users may download and use QIIME2 on Quest.

Installing QIIME2 on Quest

On Quest, QIIME2 is available for use as either a Singularity container or a conda distribution. Your day-to-day use of QIIME2 will depend on the installation route you choose. Although installing QIIME2 via Singularity is generally easier, using QIIME2 as a conda environment is advantageous in terms of code readability. Both QIIME2 installation methods take an extended period of time to complete, and wait times of over an hour are not unusual. Once QIIME2 is installed, however, there will be no waits associated with using the software.

Installation and use via Singularity

DockerHub maintains an image of the most up-to-date version of QIIME2 that can be downloaded via Singularity onto Quest. Navigate to your project directory on Quest and run the following command to pull the latest version of QIIME2 (version 2021.2 at the time of writing):

module load singularity

singularity pull --name ./qiime2_2021.2.sif docker://

This will create a Singularity Image File calledqiime2_2021.2.sifin your working directory. This file will have to be explicitly called before every QIIME2 command with singularity exec. For example, to run the qiime --help command, submit the following:

singularity exec qiime2_2021.2.sif qiime --help

It should be noted that if the above command is submitted outside of the user's working directory as written, qiime2_2021.2.sif will not be found. Please refer to our Singularity Knowledge Base page or the Singularity user documentation for more information on how to specify file paths with Singularity.

Installation and use with conda

To create a QIIME2 conda environment, first download the configuration file provided by the developers into your working directory:


This config file lists all the software dependencies that QIIME2 requires. Once it is downloaded, load the Anaconda module and create a QIIME2 conda environment

module purge all

module load python/anaconda3.6

conda env create -n qiime2-2021.2 --file qiime2-2021.2-py36-linux-conda.yml

As an optional step, you can remove the config file from your working directory:

rm qiime2-2021.2-py36-linux-conda.yml

Once the conda environment is created, use source activate to call QIIME2 (qiime2-2021.2). Afterwards, you can begin using QIIME2 by simply calling qiime:

source activate qiime2-2021.2

qiime --help

See Also:

Keywords:qiime2, qiime, microbiome, genomics   Doc ID:115055
Owner:Research Computing .Group:Northwestern
Created:2021-12-01 11:29 CDTUpdated:2021-12-08 15:12 CDT
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