QIIME (pronounced chime) stands for Quantitative Insights Into [https://en.wikipedia.org/wiki/Microbial_ecology Microbial Ecology], is an open-source [https://en.wikipedia.org/wiki/Bioinformatics bioinformatics] pipeline for performing [https://en.wikipedia.org/wiki/Microbiota microbiome] analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on [https://www.illumina.com/ Illumina] or other platforms to publication-quality graphics and statistics. This includes demultiplexing and quality filtering, [https://en.wikipedia.org/wiki/Operational_taxonomic_unit OTU] picking, taxonomic assignment, phylogenetic reconstruction, diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples. Note: QIIME 2 has replaced QIIME 1 as of January 1, 2018; version 1 is no longer supported. Note: As of February 2020, due to various issues generated by Conda environments on our HPC systems, installation using Anaconda or Miniconda is no longer supported. == QIIME2 as a module == QIIME2 is available in our environment via a module which wraps around a container. To know which versions are available, run {{Command|module spider qiime2}} After loading the module, you can run {{Command|qiime --help}} {{Callout |title=Note |content=Since the qiime command is in fact calling a container, you may have to define the environment variable APPTAINER_BIND to bind specific folders within the container to access your data. For example: APPTAINER_BIND=/home qiime ... }} === Minimal Example === A minimal example of a job submission script: {{File |name=qiime2-example.sh |lang="bash" |contents= #!/bin/bash #SBATCH --account=def-someprof # adjust this to match the accounting group you are using to submit jobs #SBATCH --mem-per-cpu=4096M # adjust this according to the memory you need #SBATCH --cpus-per-task=1 # adjust this according to the number of core you need #SBATCH --time=08:00:00 # adjust this to match the walltime of your job module load StdEnv/2023 qiime2/2024.5 # Change directory to where our data live cd $SCRATCH # https://apptainer.org/docs/user/main/appendix.html # Bind source:destination, bind current directory to /data export APPTAINER_BIND=$PWD:/data # Set the working directory to be used for /tmp, /var/tmp and $HOME export APPTAINER_WORKDIR=$SLURM_TMPDIR # run with /data mounted qiime tools import --input-path /data/input.fasta --output-path /data/output.fasta.qza --type 'FeatureData[Sequence]' }} ==Installation == QIIME2 can be installed using [[Apptainer]] or [[EasyBuild]]. Apptainer is strongly preferred since it does not generate many thousands of files in your /home directory, potentially causing you to exceed the disk quota limit on the number of files. {{Outdated}} === Using Apptainer === The QIIME2 developers publish images on [https://quay.io/organization/qiime2 Quay.io]. In order to use one of these images on our systems, you must first build an Apptainer image: {{Commands |module load apptainer |apptainer build qiime2-2021.11.sif docker://quay.io/qiime2/core:2021.11 }} This build step may take over an hour, but you only need to do this once. Save the image file (qiime2-2021.11.sif in this example) for later re-use. Then run your code as described in the [[Apptainer]] page. You will typically run each QIIME command in a apptainer exec statement: {{Commands |apptainer exec qiime2-2021.11.sif }} So your [[Running jobs|SBATCH]] script might look something like this:

#!/bin/bash
#SBATCH --time=15:00:00
#SBATCH --account=def-someuser

apptainer exec -B $PWD:/home -B /scratch/someuser:/outputs \
  -B /project/def-somePI/someuser/path/to/inputs:/inputs qiime2-2021.11.sif \
  qiime tools import --type 'FeatureData[Sequence]' \
  --input-path /inputs/some_fastafile.fa \
  --output-path /outputs/some_output_feature.qza

apptainer exec -B $PWD:/home -B /scratch/someuser:/outputs \
  -B /project/def-somePI/someuser/path/to/inputs:/inputs qiime2-2021.11.sif \
  qiime tools import \
  --type 'FeatureData[Taxonomy]' \
  --input-format HeaderlessTSVTaxonomyFormat \
  --input-path /inputs/some_taxonomy_file.tax \
  --output-path /outputs/some_output_ref-taxonomy.qza

apptainer exec -B $PWD:/home -B /scratch/someuser:/outputs \
  -B /project/def-somePI/someuser/path/to/inputs:/inputs qiime2-2021.11.sif \
  qiime feature-classifier fit-classifier-naive-bayes \
  --i-reference-reads  /outputs/some_output_feature.qza \
  --i-reference-taxonomy /outputs/some_output_ref-taxonomy.qza \
  --o-classifier /outputs/some_output_classifier.qza

Note that it is important to use the [[Apptainer#Bind_mounts|bind]] option (-B) with each folder you want to work with when you run programs in your container. For more information about Apptainer, you can watch this [https://www.youtube.com/watch?v=bpmrfVqBowY Apptainer webinar]. On first importing data into QIIME format, you may receive an error ending with a message like this:

Timezone offset does not match system offset: 0 != -18000. Please, check your config files.

This can be worked around by setting a time zone before invoking Apptainer: {{Commands |export TZ{{=}}'UTC' |apptainer exec qiime2-2021.11.sif qiime tools import ... }} =References = [http://qiime.org/ QIIME home page]
[[Category:Bioinformatics]] [[Category:User Installed Software]]