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**Current Behavior**
Hello! We would like to use Nextstrain to perform the phylogenetic analysis for the SARS-CoV-2 genomes. We have been following the tutorial on [SARS-CoV-2 Workflow](https://docs.…
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e.g., I just got the following messages:
```
2024-05-14T17:00:35.209125Z [info ] Starting pipeline as_of_date=2024-05-14 filename=assign_clades.py lineno=193 run_time=20240514T130…
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Sequences: 69
IDs ([Virus name list](https://raw.githubusercontent.com/alanrice/RSV_lineage_proposal/main/A.D.1.4X/virusNameList.txt)): EPI_ISL_19116647, EPI_ISL_19001955, EPI_ISL_19001958, EPI_ISL…
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In https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=393765&lvl=3&lin=f&keep=1&srchmode=1&unlock
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| Upvotes | 0 |
| URL | [tree.opentreeo…
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We need to have a structure to support nothotaxa, which is not contemplated by the current database design. Some things to keep in mind
- Names for nothotaxa include the multiplication sign, ×, whi…
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`--output-csv` seems to be producing `;`-sep not `,`-sep
The `--output-tsv` is fine.
```
% cd dattaset-dir
% nextclade run --input-fasta seqiences.fasta ---dataset-dir . --output-csv out.csv
…
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Hi,
I'm trying to align the genomes of these 6 species:
For Talp I have 12 resequenced genomes plus the reference, for a total of 18 genomes to align.
This is how I set the control file:
…
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Raised by @trvrb in today's [forecasting meeting](https://docs.google.com/document/d/1KOSohRX0D-jnc1HtXeQumTAm6_Nql9lhIKjvqK3hflE/edit).
Revisit the current config [thresholds in `prepare_data`](h…
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The morphological dataset has 54 hard topological constraints in a FBD dating analysis (attached). It fail to launch in both Mac (Big Sur 11.2.2) and Ubuntu (20.04.2 LTS). Mac gave "segmentation fault…