Tassy J. Bazile

Here is a piece of the output usage: bactopia datasets [-h] [--outdir STR] [--species STR] [--skip_mlst] My database directory's contents: antimicrobial-resistance minmer summary.json Thanks

Hello Robert, I reinstalled bactobia, bactopia --version gave bactopia 2.2.0 However the help gave bactopia -h bactopia download [-h] [--envtype STR] [--wf STR] [--use_defaults] [--build_all] [--build_nfcore] [--registry STR] ..... Couldn't...

Yeah it's a fresh environment. Do you refer to this one user/conda/envs/bactopia/ bin cmake compiler_compat condabin conda-meta etc fonts include lib libexec man pkgs sbin share shell ssl var x86_64-conda_cos6-linux-gnu...

Error executing process > 'BACTOPIA:GATHER_SAMPLES (brucey_v2)' Caused by: Conda prefix path does not exist or is not a directory: /color/user/conda/envs/bactopia/share/bactopia-2.2.x/conda/envs/gather_samples-2.2.x

- I am on server - As I explored singularity I got this bactopia_latest.sif How does it look? I also got this while downdloading the image INFO: Downloading library image...

Robert, Assuming the image is ok. Is there any steps before running bactopia? Thanks

Thanks, Robert! It worked TJ

Hi also have issues with python test_midas.py -vf. Could anyone have an idea about this? test_class (__main__._01_CheckEnv) ... ok test_class (__main__._02_ImportDependencies) ... ok test_class (__main__._03_CheckVersions) ... ok test_class (__main__._04_HelpText) ......

Hi Iskatz, Actually, the columns match but some of them have no values computed, such as the the coverage column. Here is the output of the column -t. First and...