Comments (8)
How did you install PopPUNK, can you copy the commands you ran?
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Can you also give the output of conda list
?
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And can you also try running:
sketchlib --version
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Sorry for my delay too, just back from holiday
What is the result of running ls $CONDA_PREFIX/lib/python3.8/site-packages
? Do you see files related to pp_sketchlib?
This is an odd one, I am guessing that the sketchlib library hasn't been installed where it's expected to be. I would suggest trying a new environment using python3.10 as a next step, but this may need a conda clearout. Another alternative could be to try the docker container on quay.io
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Related Issues (20)
- 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
- 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
- issues with assigning GPSCs HOT 4
- poppunk_visualise unable to find sequence in clustering HOT 2
- Versions of input databases sketches are different and the network file choice for Cytoscape visualization HOT 6
- distance calculations hang forever HOT 7
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