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pvdam3 / FoEC2

Fusarium oxysporum Effector Clustering version 2
MIT License
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unable to run snakemake #2

Open shanmugavadivelps opened 1 year ago

shanmugavadivelps commented 1 year ago

I could run ./foec_setup.sh -g /home/microbiology/FoEC2/16 and got the genome config file

Then i tried as you said and got error as below.

snakemake --use-singularity --use-conda --cores 6 Building DAG of jobs... WARNING: underlay of /etc/localtime required more than 50 (74) bind mounts WorkflowError: Unable to find environment in container image. Maybe a conda environment was modified without containerizing again (see snakemake --containerize)? Details: Command 'SINGULARITYENV_CONDA_PKGS_DIRS=/tmp/conda/e7040f71-b17c-43e6-88f6-846cb42aa18c singularity --quiet --silent exec --home /home/microbiology/FoEC2 /home/microbiology/FoEC2/.snakemake/singularity/29c46ba7a831b1ad5bf4a5e5d5165eb7.simg sh -c '[ -d '\''/conda-envs/50ba960368883e5775eedd03e35da544'\'' ]'' returned non-zero exit status 1. WARNING: underlay of /etc/localtime required more than 50 (74) bind mounts

pls help me to solve the issue

pvdam3 commented 1 year ago

Hi! I noticed that you are running the pipeline with --use-singularity. Could you try removing that, and just run the command as shown in the readme? https://github.com/pvdam3/FoEC2#usage

snakemake --use-conda --cores [N]