CreateCondaEnvironmentException: Could not create conda environment

[JCHmu]

When I run the virsorter run -w vs2 -i CRC_meta.fa --min-length 1500 -j 4 all code again, I get an error as CreateCondaEnvironmentException. Could not create conda environment

CreateCondaEnvironmentException: Could not create conda environment from /data1/jch/miniconda3/envs/virsorter/lib/python3.10/site-packages/virsorter/rules/../envs/vs2.yaml:

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

Traceback (most recent call last):
  File "/data1/jch/miniconda3/envs/virsorter/lib/python3.10/site-packages/conda/exception_handler.py", line 17, in __call__
    return func(*args, **kwargs)
  File "/data1/jch/miniconda3/envs/virsorter/lib/python3.10/site-packages/conda_env/cli/main.py", line 56, in do_call
    exit_code = getattr(module, func_name)(arguments, parser)
  File "/data1/jch/miniconda3/envs/virsorter/lib/python3.10/site-packages/conda/notices/core.py", line 124, in wrapper
    return func(*args, **kwargs)
  File "/data1/jch/miniconda3/envs/virsorter/lib/python3.10/site-packages/conda_env/cli/main_create.py", line 162, in execute
    result[installer_type] = installer.install(
  File "/data1/jch/miniconda3/envs/virsorter/lib/python3.10/site-packages/mamba/mamba_env.py", line 54, in mamba_install
    index = load_channels(pool, channel_urls, repos, prepend=False)
  File "/data1/jch/miniconda3/envs/virsorter/lib/python3.10/site-packages/mamba/utils.py", line 126, in load_channels
    index = get_index(
  File "/data1/jch/miniconda3/envs/virsorter/lib/python3.10/site-packages/mamba/utils.py", line 107, in get_index
    is_downloaded = dlist.download(api.MAMBA_DOWNLOAD_FAILFAST)
RuntimeError: Download error (28) Timeout was reached [https://repo.anaconda.com/pkgs/r/noarch/repodata.json.zst]
Failed to resolve host 'repo.anaconda.com' with timeout after 43149 ms

$ /data1/jch/miniconda3/envs/virsorter/bin/mamba create --quiet --file /data1/jch/db/virsorter_db/db/conda_envs/b1c7c643.yaml --prefix /data1/jch/db/virsorter_db/db/conda_envs/b1c7c643

environment variables: CIO_TEST= CONDA_AUTO_UPDATE_CONDA=false CONDA_BACKUP_ADDR2LINE=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- addr2line CONDA_BACKUP_AR=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu-ar CONDA_BACKUP_AS=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu-as CONDA_BACKUP_BUILD=x86_64-conda-linux-gnu CONDA_BACKUP_CC=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu-cc CONDA_BACKUP_CC_FOR_BUILD=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu-cc CONDA_BACKUP_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector- strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data1/jch/miniconda3/envs/deepvirfinder/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno- plt -O2 -ffunction-sections -pipe -isystem /data1/jch/miniconda3/envs/deepvirfinder/include CONDA_BACKUP_CMAKE_PREFIX_PATH=/data1/jch/miniconda3/envs/deepvirfinder:/data1/jch/miniconda3/envs/de epvirfinder/x86_64-conda-linux-gnu/sysroot/usr CONDA_BACKUP_CONDA_BUILD_SYSROOT=/data1/jch/miniconda3/envs/deepvirfinder/x86_64-conda-linux- gnu/sysroot CONDA_BACKUP_CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu CONDA_BACKUP_CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu CONDA_BACKUP_CPP=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- cpp CONDA_BACKUP_CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data1/jch/miniconda3/envs/deepvirfinder/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data1/jch/miniconda3/envs/deepvirfinder/include CONDA_BACKUP_CXX=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux- gnu-c++ CONDA_BACKUP_CXXFILT=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux- gnu-c++filt CONDA_BACKUP_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno- plt -O2 -ffunction-sections -pipe -isystem /data1/jch/miniconda3/envs/deepvirfinder/include -fvisibility-inlines- hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree- vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction- sections -pipe -isystem /data1/jch/miniconda3/envs/deepvirfinder/include CONDA_BACKUP_CXX_FOR_BUILD=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux- gnu-c++ CONDA_BACKUP_DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector- all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /data1/jch/miniconda3/envs/deepvirfinder/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /data1/jch/miniconda3/envs/deepvirfinder/include CONDA_BACKUP_DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /data1/jch/miniconda3/envs/deepvirfinder/include -D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /data1/jch/miniconda3/envs/deepvirfinder/include CONDA_BACKUP_DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /data1/jch/miniconda3/envs/deepvirfinder/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /data1/jch/miniconda3/envs/deepvirfinder/include CONDA_BACKUP_DWP=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- dwp CONDA_BACKUP_ELFEDIT=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- elfedit CONDA_BACKUP_GCC=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- gcc CONDA_BACKUP_GCC_AR=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- gcc-ar CONDA_BACKUP_GCC_NM=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- gcc-nm CONDA_BACKUP_GCC_RANLIB=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- gcc-ranlib CONDA_BACKUP_GPROF=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- gprof CONDA_BACKUP_GXX=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux- gnu-g++ CONDA_BACKUP_HOST=x86_64-conda-linux-gnu CONDA_BACKUP_LD=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu-ld CONDA_BACKUP_LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl, --disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/data1/jch/miniconda3/envs/deepvirfinder/lib -Wl,-rpath- link,/data1/jch/miniconda3/envs/deepvirfinder/lib -L/data1/jch/miniconda3/envs/deepvirfinder/lib -Wl,-O2 -Wl,--sort- common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/data1/jch/miniconda3/envs/deepvirfinder/lib -Wl,-rpath- link,/data1/jch/miniconda3/envs/deepvirfinder/lib -L/data1/jch/miniconda3/envs/deepvirfinder/lib CONDA_BACKUP_LD_GOLD=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- ld.gold CONDA_BACKUP_MESON_ARGS=--buildtype release CONDA_BACKUP_NM=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu-nm CONDA_BACKUP_OBJCOPY=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- objcopy CONDA_BACKUP_OBJDUMP=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- objdump CONDA_BACKUP_RANLIB=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- ranlib CONDA_BACKUP_READELF=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- readelf CONDA_BACKUP_SIZE=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- size CONDA_BACKUP_STRINGS=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- strings CONDA_BACKUP_STRIP=/data1/jch/miniconda3/envs/deepvirfinder/bin/x86_64-conda-linux-gnu- strip CONDA_BACKUP__CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu CONDA_BACKUP_build_alias=x86_64-conda-linux-gnu CONDA_BACKUP_host_alias=x86_64-conda-linux-gnu CONDA_DEFAULT_ENV=virsorter CONDA_EXE=/data1/jch/miniconda3/bin/conda CONDA_PREFIX=/data1/jch/miniconda3/envs/virsorter CONDA_PREFIX_1=/data1/jch/miniconda3 CONDA_PREFIX_2=/data1/jch/miniconda3/envs/deepvirfinder CONDA_PREFIX_3=/data1/jch/miniconda3/envs/vs2 CONDA_PREFIX_4=/data1/jch/miniconda3 CONDA_PROMPT_MODIFIER=(virsorter) CONDA_PYTHON_EXE=/data1/jch/miniconda3/bin/python CONDA_ROOT=/data1/jch/miniconda3/envs/virsorter CONDA_SHLVL=5 CURL_CA_BUNDLE= LD_PRELOAD= PATH=/data1/jch/miniconda3/envs/virsorter/bin:/data1/jch/miniconda3/condabi n:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/ga mes:/usr/local/games:/snap/bin:/data1/jch/db/EasyMicrobiome/linux:/dat a1/jch/db/EasyMicrobiome/script:/data1/jch/db/EasyMicrobiome REQUESTS_CA_BUNDLE= SSL_CERT_FILE=

 active environment : base
active env location : /data1/jch/miniconda3/envs/virsorter
        shell level : 5
   user config file : /home/jch/.condarc

populated config files : /home/jch/.condarc conda version : 23.7.4 conda-build version : not installed python version : 3.10.0.final.0 virtual packages : __archspec=1=x86_64 cuda=11.4=0 glibc=2.35=0 linux=5.15.0=0 unix=0=0 base environment : /data1/jch/miniconda3/envs/virsorter (writable) conda av data dir : /data1/jch/miniconda3/envs/virsorter/etc/conda conda av metadata url : None channel URLs : https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/linux-64 https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/noarch https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/linux-64 https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/noarch 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://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 : /data1/jch/miniconda3/envs/virsorter/pkgs /home/jch/.conda/pkgs envs directories : /data1/jch/miniconda3/envs/virsorter/envs /home/jch/.conda/envs platform : linux-64 user-agent : conda/23.7.4 requests/2.32.3 CPython/3.10.0 Linux/5.15.0-70-generic ubuntu/20.04.5 glibc/2.35 UID:GID : 1003:1001 netrc file : None offline mode : False

An unexpected error has occurred. Conda has prepared the above report. If you suspect this error is being caused by a malfunctioning plugin, consider using the --no-plugins option to turn off plugins.

Example: conda --no-plugins install

Alternatively, you can set the CONDA_NO_PLUGINS environment variable on the command line to run the command without plugins enabled.

Example: CONDA_NO_PLUGINS=true conda install

File "/data1/jch/miniconda3/envs/virsorter/lib/python3.10/site-packages/snakemake/deployment/conda.py", line 350, in create