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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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Bipartitions missing when transferring node label #369

Closed mesti90 closed 1 year ago

mesti90 commented 1 year ago

I have an error on some datasets when running gubbins 3.2.1. The software was called with the following command: run_gubbins.py --tree-builder fasttree --threads 30 --iterations 100 --extensive-search chromosomes.fasta

The error message: Bipartitions missing when transferring node label transfer: ['00000000000000000011....']

nickjcroucher commented 1 year ago

Thanks - can you please try upgrading to v3.3 and testing whether the issue reappears? Otherwise it may be worth changing the tree building or model fitting algorithm (e.g. to RAxML). Also --iterations 5 should be plenty, otherwise the run will take a long time!

mesti90 commented 1 year ago

Version 3.3 does not solve the issue: it still ends with the same error, except for a warning: This is a known issue when using FastTree to fit a phylogenetic model; use an alternative algorithm What can be the reason of this error? How to solve it if I'd like to use FastTree?

nickjcroucher commented 1 year ago

Fasttree cannot be used to fit a model when there are zero length branches. You can still build the tree with Fasttree, but you will need to specify a different algorithm with --model-fitter, e.g. RAxML.

From: mesti90 @.> Sent: Monday, May 22, 2023 9:38:36 PM To: nickjcroucher/gubbins @.> Cc: Croucher, Nicholas J @.>; Comment @.> Subject: Re: [nickjcroucher/gubbins] Bipartitions missing when transferring node label (Issue #369)

Version 3.3 does not solve the issue: it still ends with the same error, except for a warning: This is a known issue when using FastTree to fit a phylogenetic model; use an alternative algorithm What can be the reason of this error? How to solve it if I'd like to use FastTree?

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