[Preview] QIIME 2 2026.4 breaking changes & environment files

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Environment files for 2026.4 have been released! Please see the official announcement for more details.

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:exclamation: Important :exclamation:

The following is an early developer preview of all interface & API changes expected in 2026.4, as well as a list of our targeted environment file updates.

Changes will be added up until February 27th (for tiny & amplicon distros); we will post a formal announcement for our developer community shortly thereafter with finalized details.

Interface Changes :tv:

Plugin API Changes :electric_plug:

Environment File Changes :card_file_box:

TINY

  • biom-format=2.1.17
  • h5py=3.15.1
  • hdf5=1.14.6
  • networkx=3.6.1
  • numpy=2.4.2
  • pandas=2.3.3
  • parsl=2026.2.23
  • python=3.12
  • r-base=4.5.2
  • r-reticulate=1.45.0
  • scikit-bio=0.7.2
  • scikit-learn=1.7.1
  • scipy=1.17.1
  • tzlocal=5.3.1
  • unifrac-binaries=1.5.1
  • unifrac=1.5.1

AMPLICON (plus all changes from tiny)

  • blast=2.17.0
  • fastp=1.0.1
  • matplotlib=3.10.8
  • ncbi-datasets-pyclient=18.18.0
  • patsy=1.0.2
  • pillow=12.1.1
  • r-vegan=2.7_3
  • rpy2=3.6.4
  • samtools=1.22.1
  • seaborn=0.13.2
  • sepp=4.5.6
  • statsmodels=0.14.6
  • tqdm=4.67.3

MOSHPIT (plus all changes from tiny*)
*NOTE: The required r-base version for these updates led to a downgrade from 4.5.2 (used in tiny and amplicon) to 4.4.2. The only overlapping plugin affected in both amplicon and moshpit is q2-quality-control (via decontam). The decontam versions from both r-base releases were reviewed and showed no breaking changes, bugs, or meaningful behavioral differences, so usage of q2-quality-control should remain consistent between amplicon and moshpit.

  • bigscape=2.0.2
  • biopython=1.86
  • bowtie2=2.5.5
  • das_tool=1.1.7
  • eggnog-mapper=2.1.12
  • entrezpy=2.1.3
  • matplotlib=3.9.1
  • metabat2=2.18
  • multiqc=1.33
  • ncbi-datasets-pyclient=18.18.0
  • pyarrow=16.1.0
  • pysam=0.23.3
  • r-base=4.4.2
  • samtools=1.22.1
  • seaborn=0.13.2
  • semibin=2.2.0
  • sepp=4.5.6
  • spades=4.2.0
  • tqdm=4.67.3
  • vamb=5.0.4

PATHOGENOME (plus all changes from tiny)

  • genomad=1.11.2
  • matplotlib=3.10.8
  • prodigal=2.6.3
  • pyarrow=16.1.0
  • seaborn=0.13.2
  • screed=1.0.4
  • spades=4.2.0
  • tqdm=4.67.3
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Installing on WSL:

(base) biouser@home-PC:~$ conda env create -n qiime2-amplicon-2026.4 -f https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2026.4/amplicon/passed/qiime2-amplicon-linux-64-conda.yml

Channels:
 - conda-forge
 - bioconda
 - https://packages.qiime2.org/qiime2/2026.4/amplicon/passed
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages:
                                                                                                                                                                                        
Preparing transaction: done                                                                                                                                                             
Verifying transaction: done                                                                                                                                                             
Executing transaction: done
                                                                                                                              
ERROR conda.core.link:_execute(1033): An error occurred while installing package 'conda-forge::openmpi-4.1.6-hc5af2df_101'.                                                             
Rolling back transaction: done                                                                                                                                                          
                                                                                                                                                                                        
LinkError: post-link script failed for package conda-forge::openmpi-4.1.6-hc5af2df_101                                                                                                  
location of failed script: /home/biouser/miniconda3/envs/qiime2-amplicon-2026.4/bin/.openmpi-post-link.sh                                                                               
==> script messages <==                                                                                                                                                                 
<None>                                                                                                                                                                                  
==> script output <==                                                                                                                                                                   
stdout:                                                                                                                                                                                 
stderr:                                                                                                                                                                                 
return code: 1

I went to check /home/biouser/miniconda3/envs/qiime2-amplicon-2026.4/bin/.openmpi-post-link.sh but it was removed during the rollback.

Looks like others have got this error before. I'm using an older WSL:

(base) biouser@home-PC:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 20.04.6 LTS
Release:        20.04
Codename:       focal
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Hey @colinbrislawn,

I'm not entirely sure what the issue is here, but it looks like it's similar to what others have run into on osx with the latest version of conda. Try downgrading to conda 25.11.1 to see if this fixes the issue. That being said, these development environments are still in flux - so this may also be a transient issue that will be resolved with the final dependency updates/etc that I'm currently working on.

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Yes, installing conda 25.11 fixed it!
I saw those other threads, but forgot about them until I was back on Linux!
Thank you for your time, Liz. Feel free to split this thread, if that's helpful.

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