Listeria monocytogenes database is missing graph file.

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PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

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Listeria monocytogenes database is missing graph file. #300

Closed DOH-JDJ0303 closed 7 months ago

DOH-JDJ0303 commented 7 months ago

The Listeria monocytogenes database on bacpop.org is missing the required graph file. I have only tested this for the reference database, as the full sample set was taking too long to download. The list of files in the ref database is shown below:

  listeria_monocytogenes_v2_refs/listeria_monocytogenes_v2_refs_clusters.csv
  listeria_monocytogenes_v2_refs/listeria_monocytogenes_v2_refs.dists.npy
  listeria_monocytogenes_v2_refs/listeria_monocytogenes_v2_refs.refs
  listeria_monocytogenes_v2_refs/listeria_monocytogenes_v2_refs_unword_clusters.csv
  listeria_monocytogenes_v2_refs/listeria_monocytogenes_v2_refs_fit.pkl
  listeria_monocytogenes_v2_refs/listeria_monocytogenes_v2_refs.dists.pkl
  listeria_monocytogenes_v2_refs/listeria_monocytogenes_v2_refs.h5
  listeria_monocytogenes_v2_refs/listeria_monocytogenes_v2_refs_fit.npz

DOH-JDJ0303 commented 7 months ago

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 commented 7 months ago

Apologies for this, we will look into and update soon

DOH-JDJ0303 commented 7 months ago

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

johnlees commented 7 months ago

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 commented 7 months ago

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 commented 7 months ago

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 commented 7 months ago

Thanks again for point this out!! Also fixed