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cmkobel / CompareM2

🦠📇 Microbial genomes-to-report pipeline
https://CompareM2.readthedocs.io
GNU General Public License v3.0
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Insatlling comparem2 #111

Closed bharat1912 closed 1 day ago

bharat1912 commented 3 days ago
  1. Installed comparem2 - mamba create -c conda-forge -c bioconda -n comparem2 comparem2
  2. conda activate comparem2
  3. Ran test from E._faecium dir which contains 3 genome sequences- $comparem2

  4. Error- Using profile /pvol/opt/mambaforge/envs/comparem2/share/comparem2-2.11.1-0/profile/conda/default for setting default command line arguments. Formerly known as Assemblycomparator2
    github.com/cmkobel/comparem2/issues
    comparem2.readthedocs.io
    v2.11.1

    Variables

    title : 'E._faecium' base : '/pvol/opt/mambaforge/envs/comparem2/share/comparem2-2.11.1-0' databases : '/pvol/opt/mambaforge/envs/comparem2/share/comparem2-2.11.1-0/databases'

    Available rules

    Q.C. : copy assembly_stats sequence_lengths checkm2 busco
    Annotate : prokka bakta
    Adv. annotate : eggnog interproscan dbcan kegg_pathway abricate mlst Core-pan : panaroo
    Phylogenetic : mashtree fasttree gtdbtk iqtree treecluster snp_dists Pseudo : meta isolate downloads fast report
    (Use ´--until [..]´ to activate only one or more rules)

    Sample overview

    1-index input_file sample 1 116_2.fna 116_2 2 E8202.fna E8202 3 SRR24.fna SRR24 //

Building DAG of jobs... Creating conda environment /pvol/opt/mambaforge/envs/comparem2/share/comparem2-2.11.1-0/workflow/rules/../envs/busco.yaml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create conda environment from /pvol/opt/mambaforge/envs/comparem2/share/comparem2-2.11.1-0/workflow/rules/../envs/busco.yaml: Command: mamba env create --quiet --file "/home/ubuntu/.comparem2/conda/f295c6980d643e54c7ab7677357928f0.yaml" --prefix "/home/ubuntu/.comparem2/conda/f295c6980d643e54c7ab7677357928f0" Output: error libmamba Non-conda folder exists at prefix critical libmamba Aborting.

cmkobel commented 2 days ago

Hi bharat1912

Thanks for using CompareM2, and thanks for filing an issue.

What version of conda are you running? Could you try updating with conda update conda, and try again? You might have to reset your ~/.comparem2 directory with rm -rf ~/.comparem2.

bharat1912 commented 1 day ago

Thanks for rapid respone. Much appreciated.

I have installed the dockker version of comparem2-2.11.1-0 as I had a problem with my primary disk running out of space. I have created a docker env with mamba, installed docker and pulled comparem2 image, moved /var/lib/docker to another location which had more disk space. I am testing it out at the moment.

I will close this issue but will keep you informed.

Thanks again