Error while installing metaphor in a new device

[BioInfoStar5]

Dear colleagues, Due to limited disk space I tried to install mataphor in a new device. However, the error bellow occurred after typing command line " metaphor test". For your information, at this step no log file have been generated. Could you please help on that. Many thanks

My Terminal screenshot reported the following:

(metaphor) station2@station-HP-Z600:~/Documents/Bioinfo/tutorial-metaphor$ metaphor test Directory exists, skipping. Skipped 8 files.

Input file 'samples.csv' already exists. Skipping creation.

Starting Snakemake. This may require the installation of conda environments which should take a while.

You can suppress this confirmation message by running the Metaphor command with the -y flag.

Snakemake will start with 3 cores and 8192 MB RAM. Ok to continue? [y/N] y Your command is: snakemake \ --snakefile /home/station2/anaconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/workflow/Snakefile \ --configfile /home/station2/anaconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/test-config.yaml \ --cores 3 \ -p -r \ --use-conda --wrapper-prefix \ https://github.com/snakemake/snakemake-wrappers/raw/ --conda-prefix \ /home/station2/anaconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/conda --config Config file /home/station2/anaconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/default-config.yaml is extended by additional config specified via the command line.

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Metaphor v1.7.7 - Metagenomic Pipeline for Short Reads

© The University of Melbourne 2022 MIT licence

Documentation available at 'https://metaphor-workflow.readthedocs.io/'.

To give feedback and report bugs or issues, please go to 'https://github.com/vinisalazar/metaphor'.

Building DAG of jobs... CreateCondaEnvironmentException: The 'mamba' command is not available in the shell /bin/bash that will be used by Snakemake. You have to ensure that it is in your PATH, e.g., first activating the conda base environment with conda activate base.The mamba package manager (https://github.com/mamba-org/mamba) is a fast and robust conda replacement. It is the recommended way of using Snakemake's conda integration. It can be installed with conda install -n base -c conda-forge mamba. If you still prefer to use conda, you can enforce that by setting --conda-frontend conda. Metaphor did not finish with exit code 1. Please see the error message below. Traceback (most recent call last): File "/home/station2/anaconda3/envs/metaphor/bin/metaphor", line 10, in sys.exit(main()) ^^^^^^ File "/home/station2/anaconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/cli/cli.py", line 260, in main args.func(args) File "/home/station2/anaconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/cli/test.py", line 182, in main retcode = run_cmd(cmd) ^^^^^^^^^^^^ File "/home/station2/anaconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/utils.py", line 92, in run_cmd retcode = check_call(cmd.split()) ^^^^^^^^^^^^^^^^^^^^^^^ File "/home/station2/anaconda3/envs/metaphor/lib/python3.11/subprocess.py", line 413, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['snakemake', '--snakefile', '/home/station2/anaconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/workflow/Snakefile', '--configfile', '/home/station2/anaconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/test-config.yaml', '--cores', '3', '-p', '-r', '--use-conda', '--wrapper-prefix', 'https://github.com/snakemake/snakemake-wrappers/raw/', '--conda-prefix', '/home/station2/anaconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/conda', '--config', 'max_mb=8192']' returned non-zero exit status 1.

[vinisalazar]

Hello @BioInfoStar5,

the error message describes what must be done to fix the problem:

CreateCondaEnvironmentException: The 'mamba' command is not available in the shell /bin/bash that will be used by Snakemake. You have to ensure that it is in your PATH, e.g., first activating the conda base environment with conda activate base.The mamba package manager (https://github.com/mamba-org/mamba) is a fast and robust conda replacement. It is the recommended way of using Snakemake's conda integration. It can be installed with conda install -n base -c conda-forge mamba. If you still prefer to use conda, you can enforce that by setting --conda-frontend conda.

Please follow these steps and report back if you continue to have problems.

Thank you, Vini

[BioInfoStar5]

Thanks Vini, Yes, I tried to install mabma with: conda install -c conda-forge mamba I get this: Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed ... It took me a lot of time and never solve the environment.

Many thanks for your support

[vinisalazar]

Hi @BioInfoStar5, if installing mamba is not feasible, you can try running Metaphor with this added at the end of the command: -e " --conda-frontend conda"

Best, Vini

[vinisalazar]

I will close this issue as I don't think there's much else that can be done. Don't hesitate to reopen it if you continue to have problems.