My installation fails on "mamba env create -f conda_env.yaml". I have removed conda-forge from my channels in my ~/.condarc, but it didn't work. And then I've tried installing miniconda and mamba again, but it did not change anything. I got the following errors:

$ mamba env create -f conda_env.yaml anaconda/noarch [====================] (00m:00s) No change bioconda/noarch [====================] (00m:00s) No change bioconda/linux-64 [====================] (00m:00s) No change anaconda/linux-64 [====================] (00m:00s) No change r/linux-64 [====================] (00m:00s) No change r/noarch [====================] (00m:00s) No change pkgs/main/linux-64 [====================] (00m:00s) No change pkgs/r/linux-64 [====================] (00m:00s) No change pkgs/r/noarch [====================] (00m:00s) No change pkgs/main/noarch [====================] (00m:00s) No change ohmeta/noarch [====================] (00m:00s) No change conda-forge/noarch [====================] (00m:00s) Done ohmeta/linux-64 [====================] (00m:00s) No change conda-forge/linux-64 [====================] (00m:02s) Done

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Traceback (most recent call last):
  File "/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/lib/python3.8/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/lib/python3.8/site-packages/conda_env/cli/main_create.py", line 111, in execute
    result[installer_type] = installer.install(prefix, pkg_specs, args, env)
  File "/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/lib/python3.8/site-packages/mamba/mamba_env.py", line 42, in mamba_install
    index = load_channels(
  File "/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/lib/python3.8/site-packages/mamba/utils.py", line 135, in load_channels
    repo = subdir.create_repo(pool)
RuntimeError: Could not read JSON repodata file (/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/pkgs/cache/976d321b.json) parse error line 17356

$ /ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/bin/mamba create -f conda_env.yaml

environment variables: CIO_TEST= CONDA_AUTO_UPDATE_CONDA=false CONDA_DEFAULT_ENV=base CONDA_EXE=/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/b in/conda CONDA_PREFIX=/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3 CONDA_PROMPT_MODIFIER=(base) CONDA_PYTHON_EXE=/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/b in/python CONDA_ROOT=/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3 CONDA_SHLVL=1 LD_LIBRARY_PATH=/opt/gridengine/lib/lx-amd64:/opt/openmpi/lib:/opt/python/lib MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles PATH=/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/b in:/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda 3/condabin:/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/m iniconda3/bin:/ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv/bi n:/ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv3.6/bin:/ldfssz 1/ST_META/share/User/zhujie/.conda/envs/bioenv2/bin:/ldfssz1/ST_META/s hare/User/juyanmei/miniconda3/bin:/ldfssz1/ST_META/share/flow/biobaker y-metaphlan2-d8ab9ca4244c:/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/ local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/bio/ncbi/ bin:/opt/bio/mpiblast/bin:/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:/o pt/bio/tcoffee/bin:/opt/bio/hmmer/bin:/opt/bio/phylip/exe:/opt/bio/mrb ayes:/opt/bio/fasta:/opt/bio/glimmer/bin:/opt/bio/glimmer/scripts:/opt /bio/gromacs/bin:/opt/bio/gmap/bin:/opt/bio/tigr/bin:/opt/bio/autodock suite/bin:/opt/bio/wgs/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/jav a/latest/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/condor/bin:/opt/condo r/sbin:/opt/gridengine/bin/lx-amd64:/home/liangweiting/bin REQUESTS_CA_BUNDLE= SPATH=/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/stronginstal l SSL_CERT_FILE= ftp_proxy= http_proxy= https_proxy= no_proxy=

 active environment : base
active env location : /ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3
        shell level : 1
   user config file : /home/liangweiting/.condarc

populated config files : /home/liangweiting/.condarc conda version : 4.8.3 conda-build version : not installed python version : 3.8.3.final.0 virtual packages : __glibc=2.17 base environment : /ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/ohmeta/linux-64 https://conda.anaconda.org/ohmeta/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/pkgs envs directories : /ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/envs /home/liangweiting/.conda/envs platform : linux-64 user-agent : conda/4.8.3 requests/2.23.0 CPython/3.8.3 Linux/2.6.32-696.30.1.el6.x86_64 centos/6.9 glibc/2.17 UID:GID : 1000590:2782 netrc file : None offline mode : False

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

chrisquince / STRONG

Installation problem: RuntimeError: Could not read JSON repodata file #104

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