Installation of metaphor and testing

[sakuragi0109]

Hi,

I've installed metaphor using your description on github. However, when I run metaphor test, it always gives me the same errors:

Creating conda environment /fs04/rp24/Thanh/miniconda3/envs/metaphor_old/lib/python3.9/site-packages/metaphor/workflow/rules/../envs/vamb.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /fs04/rp24/Thanh/miniconda3/envs/metaphor_old/lib/python3.9/site-packages/metaphor/workflow/rules/../envs/vamb.yaml:
Command:
mamba env create --quiet --file "/fs04/rp24/Thanh/miniconda3/envs/metaphor_old/lib/python3.9/site-packages/metaphor/config/conda/eaeef7e323ef66f8a02878ab62e10844_.yaml" --prefix "/fs04/rp24/Thanh/miniconda3/envs/metaphor_old/lib/python3.9/site-packages/metaphor/config/conda/eaeef7e323ef66f8a02878ab62e10844_"
Output:
error libmamba Non-conda folder exists at prefix
critical libmamba Aborting.

Metaphor did not finish with exit code 1. Please see the error message below.
An error occurred while running Metaphor. Please check the traceback below.
Traceback (most recent call last):
File "/home/dinhn/rp24/Thanh/miniconda3/envs/metaphor_old/bin/metaphor", line 10, in
sys.exit(main())
File "/fs04/rp24/Thanh/miniconda3/envs/metaphor_old/lib/python3.9/site-packages/metaphor/cli/cli.py", line 278, in main
args.func(args)
File "/fs04/rp24/Thanh/miniconda3/envs/metaphor_old/lib/python3.9/site-packages/metaphor/cli/test.py", line 182, in main
retcode = run_cmd(cmd)
File "/fs04/rp24/Thanh/miniconda3/envs/metaphor_old/lib/python3.9/site-packages/metaphor/utils.py", line 92, in run_cmd
retcode = check_call(cmd.split())
File "/fs04/rp24/Thanh/miniconda3/envs/metaphor_old/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['snakemake', '--snakefile', '/fs04/rp24/Thanh/miniconda3/envs/metaphor_old/lib/python3.9/site-packages/metaphor/workflow/Snakefile', '--configfile', '/fs04/rp24/Thanh/miniconda3/envs/metaphor_old/lib/python3.9/site-packages/metaphor/config/test-config.yaml', '--cores', '3', '--printshellcmds', '--use-conda', '--wrapper-prefix', 'https://github.com/snakemake/snakemake-wrappers/raw/', '--conda-prefix', '/fs04/rp24/Thanh/miniconda3/envs/metaphor_old/lib/python3.9/site-packages/metaphor/config/conda', '--config', 'max_mb=8192']' returned non-zero exit status 1.

Until now, I haven't been able to fix it. Can you help me to fix this problem? Thank you so much!

[vinisalazar]

Hi @sakuragi0109, thank you for raising this issue.

This looks like a problem with your conda directory. The error says: error libmamba Non-conda folder exists at prefix.

By default, Metaphor creates conda environments inside the directory where Metaphor is installed, in your case: fs04/rp24/Thanh/miniconda3/envs/metaphor_old/lib/python3.9/site-packages/metaphor/config/conda/.

You can have a look at the contents of that directory to see if there's anything there that isn't supposed to be. However, I think maybe the easiest way to do this is to completely remove your metaphor_old environment and do a clean install of Metaphor.

Let me know how it goes.

V