text: user9650: 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 "Kanamycin resistance" --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 "Kanamycin resistance" --phenotype-metadata 'mycobacterium tuberculosis/kanamycin/metadata.tsv  --output data_example.kover --progress
  > ^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
  
  user339: 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)
  
original_text: 9650: <p>I am trying to replicate the results for the creator of this repo:  <a href="https://github.com/aldro61/kover2_paper" rel="nofollow noreferrer">https://github.com/aldro61/kover2_paper</a> for genotype to phenotype machine learning interpretable (decision tree) prediction.</p>
  <p>Specifically in the data section when I try to create the dataset as explained here:
  <a href="https://github.com/aldro61/kover2_paper/tree/master/data" rel="nofollow noreferrer">https://github.com/aldro61/kover2_paper/tree/master/data</a></p>
  <p>I make a directory called genomes_dir in the data directory. Then I do:</p>
  <pre><code>python download_genomes.py 'mycobacterium tuberculosis/kanamycin/metadata.tsv' genomes_dir
  </code></pre>
  <p>at the end of the download it tells me that it saved file <code>genome_paths.tsv</code> the data directory, not genomes_dir. So I run command:</p>
  <pre><code>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
  </code></pre>
  <p>and it just hangs with a prompt:</p>
  <pre><code>(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
  </code></pre>
  <p>it does nothing after hours and hours so I control-C'd to end the process.</p>
  <p>Does anyone have any idea what is happening?</p>
  <p>I also had to install this to get the datasets from PATRIC:  <a href="https://github.com/aldro61/patric_tools" rel="nofollow noreferrer">https://github.com/aldro61/patric_tools</a></p>
   339: <p>The single quote at <code>'mycobacterium</code> is not matched so the command prompt is waiting indefinitely for the command to be completed. Maybe you want <code>'mycobacterium tuberculosis/kanamycin/metadata.tsv'</code> (note closing quote)</p>
  