Comments (5)
I vaguely remember such issues in the past. could have been due to illegal characters in taxon names, number only names etc.
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Working (locally) using
raxmlHPC-PTHREADS-SSE3 -f d -T 2 -N 3 -m GTRCAT -c 25 -p 235813 -n ... -s ...
without optimising branch lengths etc. I'd be tempted to drop the optimisation step from augur. Thoughts?
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yes, we can skip the branch length part. treetime redoes those anyway.
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For the time being this has been done in branch avian
, commit 212511d
It requires testing with other flu / zika / ebola scripts before merging into master
from augur.
working on branch rejig
from augur.
Related Issues (20)
- frequencies: error with `--region` flag HOT 3
- Improve validation output to identify problematic nodes / properties
- `parse` silently removes spaces from record ids in the sequence output but not in the metadata output HOT 1
- `measurements export` does not consistently allow the strain column to be used as a grouping column
- Export schema wrongly fails on gene names starting with 'nuc' due to lookahead
- align: error message when reading a reference sequence does not completely explain the root issue
- Add schema for node-data JSONs HOT 1
- Allow custom date column name to be specified in `refine` - similar to `metadata-id-column` HOT 1
- Add docs regarding bootstraps
- Clarification on augur tree --exclude-sites masking HOT 4
- Make command line option headings linkable
- Augur export error HOT 2
- `augur align --method nextclade` should wrap `nextclade run` HOT 1
- pip/conda dependency version constraints not guaranteed in all environments
- export: Add option to extend the default lat/longs HOT 3
- Number of Nt changes is different from number of mutations (divergence)
- Use PyPI's pyright? HOT 2
- Augur 24.4.0 release
- Review Pyright rule exceptions HOT 2
- Support pandas version 2
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