Error installing qiime2 2024.10 on Windows 10

Technical Support
1

This is my first time trying to use Qiime2. I set up my laptop to use WSL, downloaded miniconda, and tried to install 2024.10 according to the instructions. However, when I run the command to download the Amplicon Distribution, I run into the following error:

(base) aiswaryaa@DESKTOP-RID57UG:~$ conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml
2 channel Terms of Service accepted
Channels:

  • released
  • conda-forge
  • bioconda
  • defaults
    Platform: linux-64
    Collecting package metadata (repodata.json): done
    Solving environment: done

Downloading and Extracting Packages:

Preparing transaction: failed

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/exception_handler.py", line 28, in __call__
    return func(*args, **kwargs)
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/cli/main.py", line 61, in main_subshell
    exit_code = do_call(args, parser)
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/cli/conda_argparse.py", line 206, in do_call
    result = getattr(module, func_name)(args, parser)
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/notices/core.py", line 141, in wrapper
    return func(*args, **kwargs)
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/cli/main_env_create.py", line 190, in execute
    result[installer_type] = installer.install(
                             ~~~~~~~~~~~~~~~~~^
        prefix, env.requested_packages, args, env
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/env/installers/conda.py", line 132, in install
    unlink_link_transaction.execute()
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/core/link.py", line 380, in execute
    self.verify()
    ~~~~~~~~~~~^^
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/common/io.py", line 87, in decorated
    return f(*args, **kwds)
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/core/link.py", line 327, in verify
    self.prepare()
    ~~~~~~~~~~~~^^
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/core/link.py", line 312, in prepare
    self.prefix_action_groups[stp.target_prefix] = self._prepare(
                                                   ~~~~~~~~~~~~~^
        self.transaction_context,
        ^^^^^^^^^^^^^^^^^^^^^^^^^
    ...<5 lines>...
        stp.neutered_specs,
        ^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/core/link.py", line 441, in _prepare
    packages_info_to_link = tuple(
        read_package_info(prec, pcrec)
        for prec, pcrec in zip(link_precs, pkg_cache_recs_to_link)
    )
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/core/link.py", line 442, in <genexpr>
    read_package_info(prec, pcrec)
    ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/gateways/disk/read.py", line 90, in read_package_info
    paths_data = read_paths_json(epd)
  File "/home/aiswaryaa/miniconda3/lib/python3.13/site-packages/conda/gateways/disk/read.py", line 166, in read_paths_json
    data = json.load(paths_json)
  File "/home/aiswaryaa/miniconda3/lib/python3.13/json/__init__.py", line 293, in load
    return loads(fp.read(),
        cls=cls, object_hook=object_hook,
        parse_float=parse_float, parse_int=parse_int,
        parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/aiswaryaa/miniconda3/lib/python3.13/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
           ~~~~~~~~~~~~~~~~~~~~~~~^^^
  File "/home/aiswaryaa/miniconda3/lib/python3.13/json/decoder.py", line 345, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
               ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/aiswaryaa/miniconda3/lib/python3.13/json/decoder.py", line 363, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

$ /home/aiswaryaa/miniconda3/bin/conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml

environment variables:
CIO_TEST=
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/aiswaryaa/miniconda3/bin/conda
CONDA_PREFIX=/home/aiswaryaa/miniconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/aiswaryaa/miniconda3/bin/python
CONDA_ROOT=/home/aiswaryaa/miniconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=
LD_PRELOAD=
PATH=/home/aiswaryaa/miniconda3/bin:/home/aiswaryaa/miniconda3/condabin:/us
r/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/
usr/local/games:/usr/lib/wsl/lib:/mnt/c/Program Files/WindowsApps/Micr
osoftCorporationII.WindowsSubsystemForLinux_2.6.1.0_x64__8wekyb3d8bbwe
:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/
mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/WINDOWS/System32/
OpenSSH:/mnt/c/Program
Files/dotnet:/mnt/c/Users/Aiswaryaa/AppData/Local/Programs/Eclipse Ado
ptium/jdk-17.0.10.7-
hotspot/bin:/mnt/c/Users/Aiswaryaa/AppData/Local/Microsoft/WindowsApps
:/mnt/c/Users/Aiswaryaa/Desktop:/mnt/c/Users/Aiswaryaa/Desktop/DLLs:/m
nt/c/Users/Aiswaryaa/Desk豴䕸ԏ:/mnt/c/Users/Aiswaryaa/Desktop/PsychoPy:/
mnt/c/Users/Ai豳띸ڮ㕈Z㓐Z:/mnt/c/Users/Aiswaryaa/AppData/Local/Programs/Mi
crosoft VS Code/bin:/snap/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=

 active environment : base
active env location : /home/aiswaryaa/miniconda3
        shell level : 1
   user config file : /home/aiswaryaa/.condarc

populated config files : /home/aiswaryaa/miniconda3/.condarc
/home/aiswaryaa/.condarc
conda version : 25.7.0
conda-build version : not installed
python version : 3.13.5.final.0
solver : libmamba (default)
virtual packages : __archspec=1=icelake
__conda=25.7.0=0
__glibc=2.39=0
__linux=6.6.87.2=0
__unix=0=0
base environment : /home/aiswaryaa/miniconda3 (writable)
conda av data dir : /home/aiswaryaa/miniconda3/etc/conda
conda av metadata url : None
channel URLs : main/linux-64

package cache : /home/aiswaryaa/miniconda3/pkgs
/home/aiswaryaa/.conda/pkgs
envs directories : /home/aiswaryaa/miniconda3/envs
/home/aiswaryaa/.conda/envs
platform : linux-64
user-agent : conda/25.7.0 requests/2.32.4 CPython/3.13.5 Linux/6.6.87.2-microsoft-standard-WSL2 ubuntu/24.04.3 glibc/2.39 solver/libmamba conda-libmamba-solver/25.4.0 libmambapy/2.0.5 aau/0.7.2 c/. s/. e/.
UID:GID : 1000:1000
netrc file : None
offline mode : False

An unexpected error has occurred. Conda has prepared the above report.
If you suspect this error is being caused by a malfunctioning plugin,
consider using the --no-plugins option to turn off plugins.

Example: conda --no-plugins install

Alternatively, you can set the CONDA_NO_PLUGINS environment variable on
the command line to run the command without plugins enabled.

Example: CONDA_NO_PLUGINS=true conda install

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I appreciate any help!

2

Hello @ap2036,

I am able to reproduce this issue. Unfortunately, I'm not sure if there is much we can do about it. It would appear as though one of the servers we are trying to download bits of the environment from is sending us some sort of corrupted garbage. I verified that our own conda channel is not the problem, and I can't do anything about any of the 3rd party channels. This will hopefully resolve itself before too long. I suggest you try again later.

1 Like
3

@ap2036 Actually one thing you can try, run conda clean --all then try again.

4

I tried this command this morning and it fixed the problem! Thank you for your help!