Closed j23414 closed 6 months ago
Good catch! If I understand correctly, phylogenetic/config/dropped_strains.txt
is used for augur filter --exclude
so it should be updated alongside 8ab810f10cc64e45a9c2baf1bf6df9d6561578bc. Looking more carefully at #12, the --sequences
input should also be updated to match the new ID values but I don't see that it was changed. Does it still work?
Correct, and yes the --sequences
input still works :D
git clone https://github.com/nextstrain/dengue.git
cd dengue/phylogenetic
nextstrain build . data/sequences_all.fasta
grep ">" data/sequences_all.fasta | head -n5
Which shows the sequences are ID'd by accession, not strain name:
>NC_075403
>NC_075435
>OQ919688
>ON123563
>ON123564
Good to know! But how did it work before #12 if the sequences were ID'd by accession
and augur filter
was using strain
as the ID column?
augur filter was using strain as the ID column?
This worked when we were still pulling strains from fauna (which also took advantage of the deduplication of strain names of fauna).
However, we shifted to using the ingest
folder and pulling data using ncbi datasets
. After ingest was merged, the data.nextstrain.org/files were updated so we could have a smooth transition.
Closed by #26
Current Behavior
Currently, strains listed in phylogenetic/config/dropped_strains.txt are not being dropped since https://github.com/nextstrain/dengue/commit/8ab810f10cc64e45a9c2baf1bf6df9d6561578bc
Expected behavior
Strains listed in
dropped_strains.txt
are not in the final phylogenetic tree.How to reproduce
Possible solution
Perhaps cherry pick a commit like:
Your environment: if browsing Nextstrain online
Your environment: if running Nextstrain locally
auspice 2.7.0
):Additional context
Add any other context about the problem here.