Comments (7)
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
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Apologies for this, we will look into and update soon
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Thank you, @johnlees. To add to this, it also appears that the Streptococcus pneumoniae and Streptococcus pyogenes reference database links are broken.
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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
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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
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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.
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Thanks again for point this out!! Also fixed
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Related Issues (20)
- visualize only query? HOT 1
- [database] A double-checked database of Neisseria meningitidis HOT 8
- Incorrect merge reporting from novel queries step HOT 1
- databases: reference only vs all genomes HOT 1
- IndexError: list index out of range (running current `master` branch) when running `poppunk_assign` HOT 25
- Add tutorial to documentation
- Update H. flu database to new sklearn version HOT 3
- ImportError: dlopen: cannot load any more object with static TLS HOT 4
- Sketchlib back end not available? HOT 8
- extract genome assemblies from database HOT 1
- What to expect for a sample that may have a mixture of two or more strains HOT 2
- PackagesNotFoundError HOT 2
- Generating jaccard distances per kmer HOT 3
- Enhancement: Assigning multiple GPSC types to mixed (meta-genome) samples HOT 2
- Zero Accessory Distances and Varied Core Distances in PopPUNK Fit Graph Analysis HOT 8
- Issue with a large Pseudomonas dataset HOT 4
- Unable to create the group "/sketches/": (Links) Object already exists HOT 2
- Cytoscape includes strains from the entire database even with the --include-files option HOT 5
- Input reference list is misformatted HOT 10
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