Hi all, I am having trouble with a dependency in the official linux yaml for 2026.1 on my local HPC. I am using conda 25.9.1 and I am version constrained by my HPC.
$ conda env create \
--name qiime2-test1 \
--file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2026.1/amplicon/released/qiime2-amplicon-ubuntu-latest-conda.yml
Channels:
- conda-forge
- bioconda
- https://packages.qiime2.org/qiime2/2026.1/amplicon/released
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- package deblur-1.1.1-pyhdfd78af_0 requires sortmerna 2.0, but none of the providers can be installed
Could not solve for environment specs
The following package could not be installed
└─ deblur =1.1.1 * is not installable because it requires
└─ sortmerna ==2.0 *, which conflicts with any installable versions previously reported.
The yaml that this url points to resolved for me as recently as 2 weeks ago but I’m not sure if my available conda version has changed or something has changed with sortmerna. I get the same error if I export the environment from my previously installed and working version and create from that file. I’ve resolved the error by removing packages depending on sortmerna from the yaml but not an ideal solution. Anyone else having this dependency error?
Hmm, this is interesting. Offhand, my initial suspicion is that this may be something related to your HPC's conda configuration - we haven't made any changes to these release environment files since they were published. But let's take a look at a few things.
My first question is regarding the solve you said you were able to get a couple of weeks ago - was this still on your institution's HPC? Or was this on a personal machine?
While on your institution's HPC, can you please run the following commands:
ldd --version
conda info
conda env list
This should give us some good starting points, information-wise.
Yes, the original solve was on the same HPC environment. It originally solved on 2026-02-17. Here is the original command used to create that environment from the conda-meta/history:
After solving the original create in February I was able to export the environment to .yaml and then Snakemake was able to successfully solve from the .yaml until very recently I started encountering the dependency error.
Here is the other information you requested:
$ ldd --version
ldd (GNU libc) 2.34
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.
$ conda info
active environment : base
active env location : /software/c/conda/25.9.1
shell level : 1
user config file : /users/wwilber/.condarc
populated config files : /software/c/conda/25.9.1/.condarc
/users/wwilber/.condarc
conda version : 25.9.1
conda-build version : not installed
python version : 3.12.12.final.0
solver : libmamba (default)
virtual packages : __archspec=1=zen3
__conda=25.9.1=0
__glibc=2.34=0
__linux=5.14.0=0
__unix=0=0
base environment : /software/c/conda/25.9.1 (read only)
conda av data dir : /software/c/conda/25.9.1/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /software/c/conda/25.9.1/pkgs
/users/wwilber/.conda/pkgs
envs directories : /users/wwilber/.conda/envs
/software/c/conda/25.9.1/envs
platform : linux-64
user-agent : conda/25.9.1 requests/2.32.5 CPython/3.12.12 Linux/5.14.0-611.42.1.el9_7.x86_64 rhel/9.7 glibc/2.34 solver/libmamba conda-libmamba-solver/25.4.0 libmambapy/2.3.3
UID:GID : 241558:241558
netrc file : None
offline mode : False
Apologies for the delayed response; thanks for providing these details.
It looks like you have environments under a few subdirectories - do you know which location you were attempting to create this new environment under (i.e. software, users/wwilber, scratch365)? One other question - which existing environment is the one you said had solved successfully, if it's still present on the system (i.e. qiime2-amplicon-2026.1, qiime2-test, etc)?
do you know which location you were attempting to create this new environment under
Yes, I’ve tried creating to both paths. My default installation path for environments I use interactively is /users/wwilber/, I use /scratch365/wwilber/ when the environment is managed by Snakemake.
which existing environment is the one you said had solved successfully, if it's still present on the system
My working environment that was previously installed is:
I came back to this today because I thought I might have some success with the 26.4 release but I’m returning the same error:
conda env create \
--name rachis-qiime2-2026.4 \
--file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2026.4/qiime2/released/rachis-qiime2-linux-64-conda.yml
Retrieving notices: done
Channels:
- conda-forge
- bioconda
- https://packages.qiime2.org/qiime2/2026.4/qiime2/released
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- package deblur-1.1.1-pyhdfd78af_0 requires sortmerna 2.0, but none of the providers can be installed
Could not solve for environment specs
The following package could not be installed
└─ deblur =1.1.1 * is not installable because it requires
└─ sortmerna ==2.0 *, which conflicts with any installable versions previously reported.
I am happily working with the 26.1 release in the environment I point to above but very strange that I can no longer install qiime2 on my HPC.
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