Comments (3)
Sorry about this, I think this looks like it's due to scikit-learn changing their API, which I couldn't make backwards compatible, see: https://github.com/bacpop/PopPUNK#2022-08-04
The change in scikit-learn's API in v1.0.0 and above mean that HDBSCAN models fitted with sklearn <=v0.24 will give an error when loaded. If you run into this, the solution is one of:
- Downgrade sklearn to v0.24.
- Run model refinement to turn your model into a boundary model instead (this will change clusters).
- Refit your model in an environment with sklearn >=v1.0.
If this is a common problem let us know, as we could write a script to 'upgrade' HDBSCAN models. See issue #213 for more details.
Was the Haemophilus_influenzae_v1_refs
database from our website? I should update it to fix this if so
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Ah sorry, I didnt see that bit in the README. Surprised that it worked on the Ubuntu box, must have used a different scikit-learn and I just didn't notice.
The database was from your website, yes. I didn't try any other ones, just that one.
C
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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
- 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
- Listeria monocytogenes database is missing graph file. HOT 7
- 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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