simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
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Run termination #87

Closed 18AS closed 3 years ago

18AS commented 3 years ago

I am getting this error report while trying to run virsorter2 after installation, database downloading and configuring. What is the issue?

CreateCondaEnvironmentException: Could not create conda environment from /home/others/bioinfo/anaconda2/envs/VS/lib/python3.6/site-packages/virsorter/rules/../envs/vs2.yaml:

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

Traceback (most recent call last):
  File "/home/others/bioinfo/anaconda2/envs/VS/lib/python3.6/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/home/others/bioinfo/anaconda2/envs/VS/lib/python3.6/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/home/others/bioinfo/anaconda2/envs/VS/lib/python3.6/site-packages/conda_env/cli/main_create.py", line 118, in execute
    result[installer_type] = installer.install(prefix, pkg_specs, args, env)
  File "/home/others/bioinfo/anaconda2/envs/VS/lib/python3.6/site-packages/mamba/mamba_env.py", line 43, in mamba_install
    pool, tuple(ordered_channels_dict.keys()), repos, prepend=False
  File "/home/others/bioinfo/anaconda2/envs/VS/lib/python3.6/site-packages/mamba/utils.py", line 99, in load_channels
    use_cache=use_cache,
  File "/home/others/bioinfo/anaconda2/envs/VS/lib/python3.6/site-packages/mamba/utils.py", line 74, in get_index
    is_downloaded = dlist.download(True)
RuntimeError: Download error (35) SSL connect error [https://conda.anaconda.org/bioconda/noarch/repodata.json]
OpenSSL SSL_connect: Connection reset by peer in connection to conda.anaconda.org:443

$ /home/others/bioinfo/anaconda2/envs/VS/bin/mamba create --quiet --file /home/others/bioinfo/AGPS/db/conda_envs/999c0136.yaml --prefix /home/others/bioinfo/AGPS/db/conda_envs/999c0136

environment variables: CIO_TEST= CONDA_AUTO_UPDATE_CONDA=false CONDA_DEFAULT_ENV=VS CONDA_EXE=/home/others/bioinfo/anaconda2/bin/conda CONDA_PREFIX=/home/others/bioinfo/anaconda2/envs/VS CONDA_PREFIX_1=/home/others/bioinfo/anaconda2 CONDA_PROMPT_MODIFIER=(VS) CONDA_PYTHON_EXE=/home/others/bioinfo/anaconda2/bin/python CONDA_ROOT=/home/others/bioinfo/anaconda2/envs/VS CONDA_SHLVL=2 CURL_CA_BUNDLE= PATH=/usr/local/qiime191:/usr/local/qiime191/bin:/usr/local/qiime191/lib:/u sr/local/qiime191/include:/home/others/bioinfo/anaconda2/envs/VS/bin:/ home/others/bioinfo/anaconda2/condabin:/usr/local/bin:/usr/bin:/usr/lo cal/sbin:/usr/sbin:/home/others/bioinfo/bin REQUESTS_CA_BUNDLE= SSL_CERT_FILE=

 active environment : base
active env location : /home/others/bioinfo/anaconda2/envs/VS
        shell level : 2
   user config file : /home/others/bioinfo/.condarc

populated config files : /home/others/bioinfo/.condarc conda version : 4.9.2 conda-build version : not installed python version : 3.6.13.final.0 virtual packages : glibc=2.17=0 unix=0=0 __archspec=1=x86_64 base environment : /home/others/bioinfo/anaconda2/envs/VS (writable) channel URLs : https://conda.anaconda.org/smaegol/linux-64 https://conda.anaconda.org/smaegol/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/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://conda.anaconda.org/au-eoed/linux-64 https://conda.anaconda.org/au-eoed/noarch https://conda.anaconda.org/biobakery/linux-64 https://conda.anaconda.org/biobakery/noarch package cache : /home/others/bioinfo/anaconda2/envs/VS/pkgs /home/others/bioinfo/.conda/pkgs envs directories : /home/others/bioinfo/anaconda2/envs/VS/envs /home/others/bioinfo/.conda/envs platform : linux-64 user-agent : conda/4.9.2 requests/2.25.1 CPython/3.6.13 Linux/3.10.0-1127.13.1.el7.x86_64 centos/7.9.2009 glibc/2.17 UID:GID : 52086:8001 netrc file : None offline mode : False

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

File "/home/others/bioinfo/anaconda2/envs/VS/lib/python3.6/site-packages/snakemake/deployment/conda.py", line 352, in create

simroux commented 3 years ago

Hi,

For VirSorter 2 errors, please file an issue in the VirSorter 2 github repo: https://github.com/jiarong/VirSorter2

That being said, the error you get seems to be a Conda error, hopefully it was a temporary one on (one of) the conda server, and it may be solved already ?

Best, Simon