CreateCondaEnvironmentException: Could not create conda environment from /VirSorter2/virsorter/rules/../envs/vs2.yaml
lifeifeifeifei opened this issue · 0 comments
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