Listeria monocytogenes database is missing graph file. about poppunk

[DOH-JDJ0303]

Adding to this the Neisseria meningitidis reference database also appears to be missing the *_fit.npz file. Below are a list of the files that come with the database.

Neisseria_meningitidis_v1_refs/Neisseria_meningitidis_v1_refs_unword_clusters.csv
  Neisseria_meningitidis_v1_refs/Neisseria_meningitidis_v1_refs_clusters.csv
  Neisseria_meningitidis_v1_refs/Neisseria_meningitidis_v1_refs.dists.pkl
  Neisseria_meningitidis_v1_refs/Neisseria_meningitidis_v1_refs.h5
  Neisseria_meningitidis_v1_refs/Neisseria_meningitidis_v1_refs.refs
  Neisseria_meningitidis_v1_refs/Neisseria_meningitidis_v1_refs.dists.npy
  Neisseria_meningitidis_v1_refs/Neisseria_meningitidis_v1_refs.refs_graph.gt

[johnlees]

Apologies for this, we will look into and update soon

[DOH-JDJ0303]

Thank you, @johnlees. To add to this, it also appears that the Streptococcus pneumoniae and Streptococcus pyogenes reference database links are broken.

[johnlees]

Thank you, @johnlees. To add to this, it also appears that the Streptococcus pneumoniae and Streptococcus pyogenes reference database links are broken.

Thanks very much for pointing this out too. This was just a typo in the website, which I've just fixed

[johnlees]

Apologies for the delays in fixing this

• Listeria database: human error copying files over (should be ok hereafter as we've since automated this). Fixed on the ftp
• Neisseria database: less clear to me what happened here as the local copy is correct, but I can confirm the download is wrong. I have replaced with the corrected version

[DOH-JDJ0303]

Hi @johnlees, thank you for fixing these but it appears there might still be one issue! The S. pyogenes reference database link appears to download the S. pneumoniae database. This is also true for the full S. pyogenes database link.

[johnlees]

Thanks again for point this out!! Also fixed