Hello,
I am nearly finished installing qiime2 on my windows laptop with a linux subsystem using ubuntu 22.04 LTS, but I'm having trouble with the last step of installing it within a conda environment. I receive the error message:
(base) peterjon123_project@LAPTOP-MAUIA3K9:~$ conda env create -n qiime2-2022.2 --file qiime2-2022.2-py38-linux-conda.yml
Collecting package metadata (repodata.json): failed
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 374, in _load
raw_repodata_str = fetch_repodata_remote_request(
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 818, in fetch_repodata_remote_request
raise Response304ContentUnchanged()
conda.core.subdir_data.Response304ContentUnchanged
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1114, in __call__
return func(*args, **kwargs)
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda_env/cli/main.py", line 80, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda_env/cli/main_create.py", line 143, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda_env/installers/conda.py", line 50, in install
unlink_link_transaction = solver.solve_for_transaction(
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 152, in solve_for_transaction
unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 195, in solve_for_diff
final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 300, in solve_final_state
ssc = self._collect_all_metadata(ssc)
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/common/io.py", line 86, in decorated
return f(*args, **kwds)
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 463, in _collect_all_metadata
index, r = self._prepare(prepared_specs)
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 1058, in _prepare
reduced_index = get_reduced_index(self.prefix, self.channels,
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/index.py", line 287, in get_reduced_index
new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 139, in query_all
result = tuple(concat(executor.map(subdir_query, channel_urls)))
File "/home/peterjon123_project/anaconda3/lib/python3.8/concurrent/futures/_base.py", line 611, in result_iterator
yield fs.pop().result()
File "/home/peterjon123_project/anaconda3/lib/python3.8/concurrent/futures/_base.py", line 439, in result
return self.__get_result()
File "/home/peterjon123_project/anaconda3/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result
raise self._exception
File "/home/peterjon123_project/anaconda3/lib/python3.8/concurrent/futures/thread.py", line 57, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 131, in <lambda>
subdir_query = lambda url: tuple(SubdirData(Channel(url), repodata_fn=repodata_fn).query(
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 144, in query
self.load()
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 209, in load
_internal_state = self._load()
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 392, in _load
_internal_state = self._read_local_repdata(mod_etag_headers.get('_etag'),
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 441, in _read_local_repdata
_internal_state = self._process_raw_repodata_str(raw_repodata_str)
File "/home/peterjon123_project/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 479, in _process_raw_repodata_str
json_obj = json.loads(raw_repodata_str or '{}')
File "/home/peterjon123_project/anaconda3/lib/python3.8/json/__init__.py", line 357, in loads
return _default_decoder.decode(s)
File "/home/peterjon123_project/anaconda3/lib/python3.8/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/home/peterjon123_project/anaconda3/lib/python3.8/json/decoder.py", line 353, in raw_decode
obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Unterminated string starting at: line 3218 column 9 (char 98156)
$ /home/peterjon123_project/anaconda3/bin/conda-env create -n qiime2-2022.2 --file qiime2-2022.2-py38-linux-conda.yml
environment variables:
CIO_TEST=
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/peterjon123_project/anaconda3/bin/conda
CONDA_PREFIX=/home/peterjon123_project/anaconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/peterjon123_project/anaconda3/bin/python
CONDA_ROOT=/home/peterjon123_project/anaconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=
PATH=/home/peterjon123_project/anaconda3/bin:/home/peterjon123_project/anac
onda3/bin:/home/peterjon123_project/anaconda3/condabin:/usr/local/sbin
:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/ga
mes:/mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.Ubuntu22.04
LTS_2204.0.10.0_x64__79rhkp1fndgsc:/mnt/c/Program Files
(x86)/Intel/iCLS Client:/mnt/c/Program Files/Intel/iCLS Client:/mnt/c/
WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WI
NDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/Program Files
(x86)/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Program
Files/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Program
Files (x86)/Intel/Intel(R) Management Engine
Components/IPT:/mnt/c/Program Files/Intel/Intel(R) Management Engine C
omponents/IPT:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Users/Owner/AppDa
ta/Local/Microsoft/WindowsApps:/snap/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
active environment : base
active env location : /home/peterjon123_project/anaconda3
shell level : 1
user config file : /home/peterjon123_project/.condarc
populated config files :
conda version : 4.13.0
conda-build version : 3.20.5
python version : 3.8.5.final.0
virtual packages : __linux=4.4.0=0
__glibc=2.35=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/peterjon123_project/anaconda3 (writable)
conda av data dir : /home/peterjon123_project/anaconda3/etc/conda
conda av metadata url : None
channel URLs : main/linux-64
main/noarch
r/linux-64
r/noarch
package cache : /home/peterjon123_project/anaconda3/pkgs
/home/peterjon123_project/.conda/pkgs
envs directories : /home/peterjon123_project/anaconda3/envs
/home/peterjon123_project/.conda/envs
platform : linux-64
user-agent : conda/4.13.0 requests/2.24.0 CPython/3.8.5 Linux/4.4.0-19041-Microsoft ubuntu/22.04 glibc/2.35
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?
No report sent. To permanently opt-out, use
$ conda config --set report_errors false
I saw there was a similar thread posted by someone else, and the suggestion there was to delete the file and redownload it. I tried that, and I didn't have any luck. Do you have any other suggestions.
Thank you,
Jonathan
forum!
