Comments (4)
Recompiled from source and now it uses fastml2 (and runs as normal). I'll post the difference in runtime (and results) once it is completed if needed.
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We are working on a fix for this, but it will be a week or two before its available.
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No problem, I convinced my installation of gubbins to use fastml2.
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FastML has been removed from version 2 of Gubbins, which should correct the problem once and for all.
https://github.com/sanger-pathogens/gubbins/tree/v2.0.0
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Related Issues (20)
- Running error of "core dumped" HOT 1
- Difference between "N" (ambiguous code ) and "-" (gap) HOT 1
- Bipartitions missing when transferring node label HOT 3
- generate_ska_alignment: error: unrecognized arguments: --input input.list HOT 10
- from numpy.core._multiarray_umath import ( KeyboardInterrupt HOT 1
- RecursionError HOT 5
- what are the best parameters that can be use for identical sequences in Raxml? HOT 1
- Dockerfile for gubbins HOT 1
- Muliple sequence alignment as input HOT 1
- Tree only shows part of the isolates HOT 5
- identifying the donor of recombination events HOT 1
- 'Palindrome middle base not W/S: 78' in generate_ska_alignment.py HOT 1
- IQtree executable name for IQtree 2.x is iqtree2 HOT 6
- alignment to use in final tree HOT 2
- alignment in final tree HOT 1
- Why are some recombination events blue but at the same loci of red ones in the same pattern in 2 distant lineages? HOT 5
- mask_gubbins_aln.py not removing recombinant regions HOT 9
- how long does joint ancestral reconstruction with pyjar take? HOT 1
- Possibility to fix the seed - for testing purpose of reproducibility ? (enhancement) HOT 2
- conda env for latest Gubbins? HOT 2
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