installation error during creating env for qiime2 2024.2

Technical Support
1

Preparing transaction: failed

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

Traceback (most recent call last):
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/exception_handler.py", line 17, in __call__
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/cli/main.py", line 83, in main_subshell
    exit_code = do_call(args, parser)
                ^^^^^^^^^^^^^^^^^^^^^
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/cli/conda_argparse.py", line 199, in do_call
    result = getattr(module, func_name)(args, parser)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/notices/core.py", line 131, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/cli/main_env_create.py", line 169, in execute
    result[installer_type] = installer.install(
                             ^^^^^^^^^^^^^^^^^^
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/env/installers/conda.py", line 62, in install
    unlink_link_transaction.execute()
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/core/link.py", line 347, in execute
    self.verify()
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/common/io.py", line 85, in decorated
    return f(*args, **kwds)
           ^^^^^^^^^^^^^^^^
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/core/link.py", line 290, in verify
    self.prepare()
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/core/link.py", line 274, in prepare
    grps = self._prepare(
           ^^^^^^^^^^^^^^
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/core/link.py", line 408, in _prepare
    packages_info_to_link = tuple(
                            ^^^^^^
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/core/link.py", line 409, in <genexpr>
    read_package_info(prec, pcrec)
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/gateways/disk/read.py", line 92, in read_package_info
    paths_data = read_paths_json(epd)
                 ^^^^^^^^^^^^^^^^^^^^
  File "/home/vidhya/miniconda3/lib/python3.12/site-packages/conda/gateways/disk/read.py", line 166, in read_paths_json
    data = json.load(paths_json)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/vidhya/miniconda3/lib/python3.12/json/__init__.py", line 293, in load
    return loads(fp.read(),
           ^^^^^^^^^^^^^^^^
  File "/home/vidhya/miniconda3/lib/python3.12/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/vidhya/miniconda3/lib/python3.12/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/vidhya/miniconda3/lib/python3.12/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

$ /home/vidhya/miniconda3/bin/conda env create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-linux-conda.yml

environment variables:
CIO_TEST=
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/vidhya/miniconda3/bin/conda
CONDA_PREFIX=/home/vidhya/miniconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/vidhya/miniconda3/bin/python
CONDA_ROOT=/home/vidhya/miniconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=
LD_PRELOAD=
PATH=/home/vidhya/miniconda3/bin:/home/vidhya/miniconda3/condabin:/usr/loca
l/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/lo
cal/games:/usr/lib/wsl/lib:/mnt/c/Program Files (x86)/Common
Files/Oracle/Java/javapath:/mnt/c/Program
Files/Java/jdk1.7.0_65/bin:/mnt/c/Program Files/NVIDIA GPU Computing
Toolkit/CUDA/v12.1/bin:/mnt/c/Program Files/NVIDIA GPU Computing
Toolkit/CUDA/v12.1/libnvvp:/mnt/c/Program Files/NVIDIA GPU Computing
Toolkit/CUDA/v12.0/bin:/mnt/c/Program Files/NVIDIA GPU Computing Toolk
it/CUDA/v12.0/libnvvp:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Wi
ndows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0:/mn
t/c/Windows/System32/OpenSSH:/mnt/c/Program
Files/dotnet:/mnt/c/Program Files (x86)/NVIDIA
Corporation/PhysX/Common:/mnt/c/Program Files/Microsoft SQL
Server/150/Tools/Binn:/mnt/c/Program Files/Microsoft SQL Server/Client
SDK/ODBC/170/Tools/Binn:/mnt/c/Program Files/PuTTY:/mnt/c/Program
Files/MySQL/MySQL Server 8.0/bin:/mnt/c/Program Files/MySQL/MySQL
Shell 8.0/bin:/mnt/c/Users/Admin/AppData/Local/Programs/Python/Python3
11/Scripts:/mnt/c/Users/Admin/AppData/Local/Programs/Python/Python311:
/mnt/c/Users/Admin/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/Ad
min/.dotnet/tools:/mnt/d/Vidhya/softwares/uppaal64-4.1.26-2/uppaal64-
4.1.26-2/bin-Windows:/mnt/d/Vidhya/softwares/uppaal64-4.1.26-
2/uppaal64-4.1.26-2/bin-
Windows:/mnt/c/Users/Admin/AppData/Local/GitHubDesktop/bin:/snap/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=

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

populated config files :
conda version : 24.3.0
conda-build version : not installed
python version : 3.12.1.final.0
solver : libmamba (default)
virtual packages : __archspec=1=icelake
__conda=24.3.0=0
__glibc=2.35=0
__linux=5.15.146.1=0
__unix=0=0
base environment : /home/vidhya/miniconda3 (writable)
conda av data dir : /home/vidhya/miniconda3/etc/conda
conda av metadata url : None
channel URLs : main/linux-64
main/noarch
r/linux-64
r/noarch
package cache : /home/vidhya/miniconda3/pkgs
/home/vidhya/.conda/pkgs
envs directories : /home/vidhya/miniconda3/envs
/home/vidhya/.conda/envs
platform : linux-64
user-agent : conda/24.3.0 requests/2.31.0 CPython/3.12.1 Linux/5.15.146.1-microsoft-standard-WSL2 ubuntu/22.04.3 glibc/2.35 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.3
UID:GID : 1000:1000
netrc file : None
offline mode : False

An unexpected error has occurred. Conda has prepared the above report.
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2

@Vidhya_Gopalakrishna That looks like there may have been an issue with the environment file you tried to use. Can you try deleting it and re-downloading it then attempting to create the environment again and posting the steps you go through and the commands you run along the way here?

4

thanks will check and revert back

5

after deleting qiime2 and run again also showing same error. i am using windows subsystem for linux

6

Can you run conda config --show-sources and post the result of that command here? That ought to echo out your .condarc if you have one.