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a-h-b / binny

GNU General Public License v3.0
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snakemake.exceptions.CreateCondaEnvironmentException #63

Open MiracleEaTu opened 2 weeks ago

MiracleEaTu commented 2 weeks ago

When I was trying to install binny using default settings: ./binny -i config/config.init.yaml I got this error message:

Full Traceback (most recent call last):
  File "/home/qijie/binny/conda/snakemake_env/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 590, in create
    out = create_env(env_file, filetype="yaml")
  File "/home/qijie/binny/conda/snakemake_env/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 552, in create_env
    out = shell.check_output(
  File "/home/qijie/binny/conda/snakemake_env/lib/python3.8/site-packages/snakemake/shell.py", line 63, in check_output
    return sp.check_output(cmd, shell=True, executable=executable, **kwargs)
  File "/home/qijie/binny/conda/snakemake_env/lib/python3.8/subprocess.py", line 415, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/home/qijie/binny/conda/snakemake_env/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'mamba env create --quiet --file "/home/qijie/binny/conda/5a076611065aff8cc31a351d4096a416_.yaml" --prefix "/home/qijie/binny/conda/5a076611065aff8cc31a351d4096a416_"' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/qijie/binny/conda/snakemake_env/lib/python3.8/site-packages/snakemake/__init__.py", line 736, in snakemake
    success = workflow.execute(
  File "/home/qijie/binny/conda/snakemake_env/lib/python3.8/site-packages/snakemake/workflow.py", line 924, in execute
    dag.create_conda_envs(
  File "/home/qijie/binny/conda/snakemake_env/lib/python3.8/site-packages/snakemake/dag.py", line 319, in create_conda_envs
    env.create(dryrun)
  File "/home/qijie/binny/conda/snakemake_env/lib/python3.8/site-packages/snakemake/deployment/conda.py", line 609, in create
    raise CreateCondaEnvironmentException(
snakemake.exceptions.CreateCondaEnvironmentException: Could not create conda environment from /home/qijie/binny/workflow/envs/binny_linux.yaml:
Command:
mamba env create --quiet --file "/home/qijie/binny/conda/5a076611065aff8cc31a351d4096a416_.yaml" --prefix "/home/qijie/binny/conda/5a076611065aff8cc31a351d4096a416_"
Output:
error    libmamba Non-conda folder exists at prefix
critical libmamba Aborting.

CreateCondaEnvironmentException:
Could not create conda environment from /home/qijie/binny/workflow/envs/binny_linux.yaml:
Command:
mamba env create --quiet --file "/home/qijie/binny/conda/5a076611065aff8cc31a351d4096a416_.yaml" --prefix "/home/qijie/binny/conda/5a076611065aff8cc31a351d4096a416_"
Output:
error    libmamba Non-conda folder exists at prefix
critical libmamba Aborting.

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Please advise how to install binny correctly, thank you!

MiracleEaTu commented 2 weeks ago

And on the other hand, if I manually run mamba env create --quiet --file "/home/qijie/binny/conda/5a076611065aff8cc31a351d4096a416_.yaml" --prefix "/home/qijie/binny/conda/5a076611065aff8cc31a351d4096a416_", It worked perfectly.. Very weird and the same problem showed up in two separate computers..