rrwick / Porechop

adapter trimmer for Oxford Nanopore reads
GNU General Public License v3.0
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porechop installation error #98

Open saassli21 opened 5 months ago

saassli21 commented 5 months ago

I can't install porechop using conda I already have my conda env activated but when I run : conda install -c bioconda porechop I have this error :

Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): failed

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

Traceback (most recent call last):
  File "/opt/conda/lib/python3.10/site-packages/conda/exceptions.py", line 1132, in __call__
    return func(*args, **kwargs)
  File "/opt/conda/lib/python3.10/site-packages/conda/cli/main.py", line 69, in main_subshell
    exit_code = do_call(args, p)
  File "/opt/conda/lib/python3.10/site-packages/conda/cli/conda_argparse.py", line 122, in do_call
    return getattr(module, func_name)(args, parser)
  File "/opt/conda/lib/python3.10/site-packages/conda/notices/core.py", line 121, in wrapper
    return func(*args, **kwargs)
  File "/opt/conda/lib/python3.10/site-packages/conda/cli/main_install.py", line 20, in execute
    install(args, parser, 'install')
  File "/opt/conda/lib/python3.10/site-packages/conda/cli/install.py", line 264, in install
    unlink_link_transaction = solver.solve_for_transaction(
  File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 134, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
  File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 177, in solve_for_diff
    final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
  File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 282, in solve_final_state
    ssc = self._collect_all_metadata(ssc)
  File "/opt/conda/lib/python3.10/site-packages/conda/common/io.py", line 84, in decorated
    return f(*args, **kwds)
  File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 449, in _collect_all_metadata
    index, r = self._prepare(prepared_specs)
  File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 1064, in _prepare
    reduced_index = get_reduced_index(self.prefix, self.channels,
  File "/opt/conda/lib/python3.10/site-packages/conda/core/index.py", line 267, in get_reduced_index
    new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
  File "/opt/conda/lib/python3.10/site-packages/conda/core/subdir_data.py", line 169, in query_all
    result = tuple(chain.from_iterable(executor.map(subdir_query, channel_urls)))
  File "/opt/conda/lib/python3.10/concurrent/futures/_base.py", line 621, in result_iterator
    yield _result_or_cancel(fs.pop())
  File "/opt/conda/lib/python3.10/concurrent/futures/_base.py", line 319, in _result_or_cancel
    return fut.result(timeout)
  File "/opt/conda/lib/python3.10/concurrent/futures/_base.py", line 458, in result
    return self.__get_result()
  File "/opt/conda/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
    raise self._exception
  File "/opt/conda/lib/python3.10/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/opt/conda/lib/python3.10/site-packages/conda/core/subdir_data.py", line 158, in subdir_query
    return tuple(
  File "/opt/conda/lib/python3.10/site-packages/conda/core/subdir_data.py", line 174, in query
    self.load()
  File "/opt/conda/lib/python3.10/site-packages/conda/core/subdir_data.py", line 264, in load
    _internal_state = self._load()
  File "/opt/conda/lib/python3.10/site-packages/conda/core/subdir_data.py", line 315, in _load
    cache.load_state()  # XXX should this succeed even if FileNotFound?
  File "/opt/conda/lib/python3.10/site-packages/conda/gateways/repodata/__init__.py", line 570, in load_state
    self.load(state_only=True)
  File "/opt/conda/lib/python3.10/site-packages/conda/gateways/repodata/__init__.py", line 528, in load
    state = json.loads(state_file.read())
  File "/opt/conda/lib/python3.10/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
  File "/opt/conda/lib/python3.10/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/opt/conda/lib/python3.10/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)

$ /opt/conda/bin/conda install -c bioconda porechop

environment variables: CIO_TEST= CONDA_DEFAULT_ENV=variants_env CONDA_EXE=/opt/conda/bin/conda CONDA_PREFIX=/opt/conda/envs/variants_env CONDA_PROMPT_MODIFIER=(variants_env) CONDA_PYTHON_EXE=/opt/conda/bin/python CONDA_ROOT=/opt/conda CONDA_SHLVL=1 CURL_CA_BUNDLE= JAVA_LD_LIBRARY_PATH=/opt/conda/envs/variants_env/lib/jvm/lib/server LD_PRELOAD= PATH=/opt/conda/envs/variants_env/bin:/home/.openvscode-server/bin/remote-c li:/opt/conda/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/b in:/sbin:/bin REQUESTS_CA_BUNDLE= SSL_CERT_FILE=

 active environment : variants_env
active env location : /opt/conda/envs/variants_env
        shell level : 1
   user config file : /root/.condarc

populated config files : /opt/conda/.condarc conda version : 23.3.1 conda-build version : not installed python version : 3.10.12.final.0 virtual packages : __archspec=1=x86_64 glibc=2.31=0 linux=5.15.0=0 __unix=0=0 base environment : /opt/conda (writable) conda av data dir : /opt/conda/etc/conda conda av metadata url : None channel URLs : https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch package cache : /opt/conda/pkgs /root/.conda/pkgs envs directories : /opt/conda/envs /root/.conda/envs platform : linux-64 user-agent : conda/23.3.1 requests/2.31.0 CPython/3.10.12 Linux/5.15.0-1054-azure ubuntu/20.04.6 glibc/2.31 UID:GID : 0:0 netrc file : None offline mode : False

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