================================================================================================================================= Developed by: Francisco Zorrilla, Kiran R. Patil, and Aleksej Zelezniak Publication: doi.org/10.1101/2020.12.31.424982/\\\/\\\\/\**/\_ ____/\//////////\/\///////////\/\_/\\ /\/\\/\\/\//\/\//\ __/\_/\/\\/\\\/\\_\/\/\\\/\\\__\/\///\/\/\/\ /\///\\///\/\/////\\////\////_\////////\_\/\**\/////\\/\///////\/\\///\/\/\_ __\/\\//\_\/\/\\\___\/\_/\\_\/\___\/\\/\\/\_\///\/\_ \/\_\/\\/\\//\///////_\/\/_/\/////\\/\\/\\/\\/\_\/\ __\/\_\/\\/\_\//\\_\//\__\//\\/_\//\\\/\/\\\\\/\_\/\ **__\///\///\///_\//////////_**\/////\////////\//_\////////////____\///////////////_\///\///

A Snakemake-based pipeline desinged to predict metabolic interactions directly from metagenomics data using high performance computer clusters

Version: 1.0.5

Setting current directory to root in config.yaml file ...

sed：无法读取 config.yaml：没有那个文件或目录 Checking if conda is available ...

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

Traceback (most recent call last):
  File "/usr/lib/python3.6/site-packages/conda/exceptions.py", line 1003, in __call__
    return func(*args, **kwargs)
  File "/usr/lib/python3.6/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/usr/lib/python3.6/site-packages/conda/cli/conda_argparse.py", line 82, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/usr/lib/python3.6/site-packages/conda/cli/main_list.py", line 142, in execute
    show_channel_urls=context.show_channel_urls)
  File "/usr/lib/python3.6/site-packages/conda/cli/main_list.py", line 80, in print_packages
    show_channel_urls=show_channel_urls)
  File "/usr/lib/python3.6/site-packages/conda/cli/main_list.py", line 45, in list_packages
    installed = sorted(PrefixData(prefix, pip_interop_enabled=True).iter_records(),
  File "/usr/lib/python3.6/site-packages/conda/core/prefix_data.py", line 117, in iter_records
    return itervalues(self._prefix_records)
  File "/usr/lib/python3.6/site-packages/conda/core/prefix_data.py", line 146, in _prefix_records
    return self.__prefix_records or self.load() or self.__prefix_records
  File "/usr/lib/python3.6/site-packages/conda/core/prefix_data.py", line 70, in load
    self._load_site_packages()
  File "/usr/lib/python3.6/site-packages/conda/core/prefix_data.py", line 261, in _load_site_packages
    python_record = read_python_record(self.prefix_path, af, python_pkg_record.version)
  File "/usr/lib/python3.6/site-packages/conda/gateways/disk/read.py", line 253, in read_python_record
    paths_tups = pydist.get_paths()
  File "/usr/lib/python3.6/site-packages/conda/common/pkg_formats/python.py", line 268, in get_paths
    records = sorted(concatv(records, ((pf, None, None) for pf in missing_pyc_files)))
TypeError: '<' not supported between instances of 'str' and 'NoneType'

$ /usr/bin/conda list

environment variables: CIO_TEST= CONDA_DEFAULT_ENV=metagem CONDA_EXE=/usr2/people/ruiwenhu/miniconda3/bin/conda CONDA_PREFIX=/usr2/people/ruiwenhu/miniconda3/envs/metagem CONDA_PREFIX_1=/usr2/people/ruiwenhu/miniconda3 CONDA_PROMPT_MODIFIER=(metagem) CONDA_PYTHON_EXE=/usr2/people/ruiwenhu/miniconda3/bin/python CONDA_ROOT=/usr/share/conda CONDA_SHLVL=2 GTDBTK_DATA_PATH=/usr2/people/ruiwenhu/miniconda3/envs/metagem/share/gtdbtk-1.7.0/db/ MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles PATH=/usr2/people/ruiwenhu/miniconda3/envs/metagem/bin:/usr/lib64/qt-3.3/bi n:/usr/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr 2/people/ruiwenhu/cplex/cplex/bin/x86-64_linux:/usr2/people/ruiwenhu/c plex/cpoptimizer/bin/x86-64_linux QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins REQUESTS_CA_BUNDLE= SSL_CERT_FILE=

 active environment : /usr2/people/ruiwenhu/miniconda3/envs/metagem
active env location : /usr2/people/ruiwenhu/miniconda3/envs/metagem
        shell level : 2
   user config file : /usr2/people/ruiwenhu/.condarc

populated config files : /usr/share/conda/condarc.d/defaults.yaml /usr2/people/ruiwenhu/.condarc conda version : 4.6.14 conda-build version : not installed python version : 3.6.8.final.0 base environment : /usr (read only) channel URLs : https://conda.anaconda.org/ursky/linux-64 https://conda.anaconda.org/ursky/noarch 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 https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /var/cache/conda/pkgs /usr2/people/ruiwenhu/.conda/pkgs envs directories : /usr2/people/ruiwenhu/.conda/envs /usr/envs platform : linux-64 user-agent : conda/4.6.14 requests/2.14.2 CPython/3.6.8 Linux/3.10.0-1160.15.2.el7.x86_64 centos/7.9.2009 glibc/2.17 UID:GID : 19524:100 netrc file : None offline mode : False

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

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WARNING: Conda is not available! Please load your cluster's conda module or install locally.

franciscozorrilla / metaGEM

Getting the following error while running the bash metaGEM.sh -t check #141

A Snakemake-based pipeline desinged to predict metabolic interactions directly from metagenomics data using high performance computer clusters

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