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dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system
https://dib-lab.github.io/elvers/
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CreateCondaEnvironmentException: Could not create conda environment from /VirSorter2/virsorter/rules/../envs/vs2.yaml #163

Closed lifeifeifeifei closed 2 years ago

lifeifeifeifei commented 2 years ago

I install the virsorter2 as suggested:

> conda create -n vs2 -c conda-forge -c bioconda "python>=3.6" scikit-learn=0.22.1 imbalanced-learn pandas seaborn hmmer==3.3 prodigal screed ruamel.yaml "snakemake>=5.18,<=5.26" click mamba
> conda activate vs2
> git clone https://github.com/jiarong/VirSorter2.git
> cd VirSorter2
> pip install -e .

> tar -xzf db.tgz
> virsorter config --init-source --db-dir=./db

but when I run it on a test dataset, it always report error.

$ virsorter run -w test.out -i test.fa --min-length 1500 -j 4 all [2021-10-11 08:04 INFO] VirSorter 2.2.3 [2021-10-11 08:04 INFO] /Software/anaconda3/envs/vs2/bin/virsorter run -w test.out -i test.fa --min-length 1500 -j 4 all [2021-10-11 08:04 INFO] Using /Software/VirSorter2/virsorter/template-config.yaml as config template [2021-10-11 08:04 INFO] conig file written to /test.out/config.yaml

[2021-10-11 08:04 INFO] Executing: snakemake --snakefile /Software/VirSorter2/virsorter/Snakefile --directory /test.out --jobs 4 --configfile /test.out/config.yaml --latency-wait 600 --rerun-incomplete --nolock --conda-frontend mamba --conda-prefix /Software/VirSorter2/db/conda_envs --use-conda --quiet all
CreateCondaEnvironmentException: Could not create conda environment from /Software/VirSorter2/virsorter/rules/../envs/vs2.yaml:

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

Traceback (most recent call last):
  File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda_env/cli/main.py", line 80, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/conda_env/cli/main_create.py", line 141, in execute
    result[installer_type] = installer.install(prefix, pkg_specs, args, env)
  File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/mamba_env.py", line 42, in mamba_install
    index = load_channels(pool, channel_urls, repos, prepend=False)
  File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/utils.py", line 123, in load_channels
    index = get_index(
  File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/mamba/utils.py", line 104, in get_index
    is_downloaded = dlist.download(True)
RuntimeError: Multi-download failed.

$ /Software/anaconda3/envs/vs2/bin/mamba create --quiet --file /Software/VirSorter2/db/conda_envs/7cf0ba25.yaml --prefix /Software/VirSorter2/db/conda_envs/7cf0ba25

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

File "/Software/anaconda3/envs/vs2/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 350, in create