hAMRonization_workflow

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- test folder, get data bash script - run test yml file

cimendes

KeyError in line 16 of hAMRonization_workflow/rules/staramr.smk: 'pointfinder'

1

Hi, after running: `git clone https://github.com/pha4ge/hAMRonization_workflow` `conda env create -n hamronization_workflow --file envs/hamronization_workflow.yaml` `conda activate hamronization_workflow` `snakemake --configfile config/config.yaml --use-conda --jobs 2 --use-singularity --singularity-args "-B $PWD:/data"` I'm getting the error:...

SvetlanaUP

`kma` silently fails when executed by `kmerresistance`: specifically no error just a non-zero exit code and no output. I can only reproduce this in the container (based off debian) and...

fmaguire

Hello everybody, I have the following error: (hamronization_workflow) kayobianco@unixkayo:~/hAMRonization_workflow$ ./run_test.sh Assuming unrestricted shared filesystem usage. host: unixkayo Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 (use --colors to...

kayobianco

Activating conda environment: .snakemake/conda/5d8473ea092af8eb4c5ecabee5c39052_ Select jobs to execute... RuleException: CalledProcessError in file "/home/ideshi/hAMRonization_workflow/rules/resfinder.smk", line 45: Command 'source /home/ideshi/anaconda3/bin/activate '/home/ideshi/hAMRonization_workflow/.snakemake/conda/5d8473ea092af8eb4c5ecabee5c39052_'; set -euo pipefail; mkdir -p results/NDM_biosample/resfinder-fna run_resfinder.py --acquired --point --disinfectant --species...

ideshigenomics