jiarong / VirSorter2

customizable pipeline to identify viral sequences from (meta)genomic data
GNU General Public License v2.0
227 stars 31 forks source link

create conda environment error #115

Closed XiongGZ closed 2 years ago

XiongGZ commented 2 years ago

When i try to test virsorter2 using command: virsorter run -w test.out -i 8seq.fa --min-length 1500 -j 4 all

I got a error report:

[2022-07-22 23:35 INFO] VirSorter 2.2.3
[2022-07-22 23:35 INFO] /home/xiongguangzhou/Software/miniconda3/envs/virsorter2/bin/virsorter run -w test.out -i 8seq.fa --min-length 1500 -j 4 all
[2022-07-22 23:35 INFO] Using /home/xiongguangzhou/Software/VirSorter2/virsorter/template-config.yaml as config template
[2022-07-22 23:35 INFO] conig file written to /home/xiongguangzhou/Software/VirSorter2/test/test.out/config.yaml

[2022-07-22 23:35 INFO] Executing: snakemake --snakefile /home/xiongguangzhou/Software/VirSorter2/virsorter/Snakefile --directory /home/xiongguangzhou/Software/VirSorter2/test/test.out --jobs 4 --configfile /home/xiongguangzhou/Software/VirSorter2/test/test.out/config.yaml --latency-wait 600 --rerun-incomplete --nolock  --conda-frontend mamba --conda-prefix /home/xiongguangzhou/Database/VirSorter2/conda_envs --use-conda    --quiet  all   
CreateCondaEnvironmentException:
Could not create conda environment from /home/xiongguangzhou/Software/VirSorter2/virsorter/rules/../envs/vs2.yaml:
Traceback (most recent call last):
  File "/home/xiongguangzhou/Software/miniconda3/envs/virsorter2/bin/mamba", line 7, in <module>
    from mamba.mamba import
  File "/home/xiongguangzhou/Software/miniconda3/envs/virsorter2/lib/python3.8/site-packages/mamba/mamba.py", line 52, in <module>
    import mamba.mamba_api as api
ImportError: /home/xiongguangzhou/Software/miniconda3/envs/virsorter2/lib/python3.8/site-packages/mamba/mamba_api.cpython-38-x86_64-linux-gnu.so: undefined symbol: curl_url_cleanup

  File "/home/xiongguangzhou/Software/miniconda3/envs/virsorter2/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 350, in create

Can you @jiarong help me? Thanks !

jiarong commented 2 years ago

Did you get error when installing the database? (virsorter setup)

XiongGZ commented 2 years ago

The database installed using virsorter setup is incomplete, so i download from https://osf.io/v46sc/download . When i try to run virsorter setup again, i get the same error.

XiongGZ commented 2 years ago

I solve the problem by reinstalling mamba. Thanks !