Problems replicating Kover paper results I am trying to replicate the results for the creator of this repo:  https://github.com/aldro61/kover2_paper for genotype to phenotype machine learning interpretable (decision tree) prediction.
Specifically in the data section when I try to create the dataset as explained here:
https://github.com/aldro61/kover2_paper/tree/master/data
I make a directory called genomes_dir in the data directory. Then I do:
python download_genomes.py 'mycobacterium tuberculosis/kanamycin/metadata.tsv' genomes_dir

at the end of the download it tells me that it saved file genome_paths.tsv the data directory, not genomes_dir. So I run command:
kover dataset create from-tsv --genomic-data genome_paths.tsv ---phenotype-description &quot;Kanamycin resistance&quot; --phenotype-metadata 'mycobacterium tuberculosis/kanamycin/metadata.tsv  --output data_example.kover --progress

and it just hangs with a prompt:
(kover) nobu@gold3forever:~/Desktop/BioInformatics/ResearchAssistant/kover2_paper/data$ kover dataset create from-tsv --genomic-data genome_paths.tsv ---phenotype-description &quot;Kanamycin resistance&quot; --phenotype-metadata 'mycobacterium tuberculosis/kanamycin/metadata.tsv  --output data_example.kover --progress
&gt; ^C

it does nothing after hours and hours so I control-C'd to end the process.
Does anyone have any idea what is happening?
I also had to install this to get the datasets from PATRIC:  https://github.com/aldro61/patric_tools
The single quote at 'mycobacterium is not matched so the command prompt is waiting indefinitely for the command to be completed. Maybe you want 'mycobacterium tuberculosis/kanamycin/metadata.tsv' (note closing quote)