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bacpop / PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
https://www.bacpop.org/poppunk
Apache License 2.0
89 stars 18 forks source link

Don't try and make trees with fewer than three samples #151

Closed johnlees closed 3 years ago

johnlees commented 3 years ago

Fixes azure error with singleton strains:

2021-02-07T14:38:27.129504570Z: [ERROR]      resp = make_response(f(*args, **kwargs))
2021-02-07T14:38:27.129508270Z: [ERROR]    File "/home/poppunk-usr/app/PopPUNK/web.py", line 94, in sketchAssign
2021-02-07T14:38:27.129512170Z: [ERROR]      generate_visualisations(outdir,
2021-02-07T14:38:27.129515870Z: [ERROR]    File "/home/poppunk-usr/app/PopPUNK/visualise.py", line 375, in generate_visualisations
2021-02-07T14:38:27.129519770Z: [ERROR]      nj_tree = generate_nj_tree(core_distMat,
2021-02-07T14:38:27.129523470Z: [ERROR]    File "/home/poppunk-usr/app/PopPUNK/trees.py", line 153, in generate_nj_tree
2021-02-07T14:38:27.129527370Z: [ERROR]      tree.reroot_at_midpoint(update_bipartitions=True, suppress_unifurcations=False)
2021-02-07T14:38:27.129531270Z: [ERROR]    File "/home/poppunk-usr/app/env/lib/python3.9/site-packages/dendropy/datamodel/treemodel.py", line 5036, in reroot_at_midpoint
2021-02-07T14:38:27.129535270Z: [ERROR]      maxtax1, maxtax2 = pdm.max_pairwise_distance_taxa()
2021-02-07T14:38:27.129542970Z: [ERROR]  TypeError: cannot unpack non-iterable NoneType object