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ZARP-cli fails when conda's channel priority is set to strict:
LibMambaUnsatisfiableError: Encountered problems while solving: - package htsinfer-0.11.0-pyhdfd78af_0 requires biopython >=1.78, but none of the providers can be installedCould not solve for environment specsThe following package could not be installed└─ htsinfer 0.11.0** is not installable because it requires └─ biopython >=1.78 , which conflicts with any installable versions previously reported.
Start ZARP-cli example run with zarp SRR23590181 SRR23529108
Expected behavior
A clear and concise description of what you expected to happen.
ZARP-cli finishes without issues.
System
OS: Ubuntu
Version 24.04
Additional context
Add any other context about the problem here.
Comprehensive error messages:
INFO Inferring metadata...CreateCondaEnvironmentException:Could not create conda environment from /path/to/zarp/workflow/rules/../envs/htsinfer.yaml:Command:mamba env create --quiet --file "/path/to/.zarp/htsinfer/.snakemake/conda/c1bf96f9b4b753f56e7729c3610e5c1f_.yaml" --prefix "/path/to/.zarp/htsinfer/.snakemake/conda/c1bf96f9b4b753f56e7729c3610e5c1f_"Output:Channels: - bioconda - conda-forgePlatform: linux-64Collecting package metadata (repodata.json): ...working... doneSolving environment: ...working... warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITYwarning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITYfailedChannels: - bioconda - conda-forgePlatform: linux-64Collecting package metadata (repodata.json): ...working... doneSolving environment: ...working... warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITYwarning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITYfailedLibMambaUnsatisfiableError: Encountered problems while solving: - package htsinfer-0.11.0-pyhdfd78af_0 requires biopython >=1.78, but none of the providers can be installedCould not solve for environment specsThe following package could not be installed└─ htsinfer 0.11.0** is not installable because it requires └─ biopython >=1.78 , which conflicts with any installable versions previously reported.MM-DD HH:MM:SS ERROR Command '['snakemake', '--printshellcmds', '--snakefile', cli.py:105 '/path/to/zarp/workflow/rules/htsinfer.smk', '--cores', '4', '--directory', '/path/to/.zarp/htsinfer', '--configfile', '/path/to/.zarp/htsinfer/runs/3AMP1E/config.yaml', '--use-conda']' returned non-zero exit status 1. DEBUG Traceback (most recent call last): cli.py:106 File "/path/to/zarp-cli/zarp/cli.py", line 102, in main samples = zarp.process_samples() File "/path/to/zarp-cli/zarp/zarp.py", line 120, in process_samples df = processor_htsinfer.process( File "/path/to/zarp-cli/zarp/plugins/sample_processo rs/htsinfer.py", line 64, in process executor.run(cmd=cmd) File "/path/to/zarp-cli/zarp/snakemake/run.py", line 108, in run raise exc File "/path/to/zarp-cli/zarp/snakemake/run.py", line 104, in run subprocess.run(cmd, check=True) File "/path/to/miniforge3/envs/zarp-cli/lib/python3.10/s ubprocess.py", line 524, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['snakemake', '--printshellcmds', '--snakefile', '/path/to/zarp/workflow/rules/htsinfer.smk', '--cores', '4', '--directory', '/path/to/.zarp/htsinfer', '--configfile', '/path/to/.zarp/htsinfer/runs/3AMP1E/config.yaml', '--use-conda']' returned non-zero exit status 1.
The text was updated successfully, but these errors were encountered:
Describe the bug
ZARP-cli fails when
conda
's channel priority is set to strict:To Reproduce
Steps to reproduce the behavior:
conda config --set channel_priority strict
zarp SRR23590181 SRR23529108
Expected behavior
A clear and concise description of what you expected to happen.
ZARP-cli finishes without issues.
System
Additional context
Add any other context about the problem here.
Comprehensive error messages:
The text was updated successfully, but these errors were encountered: