Freyja update doesn't provide the latest version of usher_barcodes.feather and lineage_mutations.json

[mariemoinet]

I realised I was working with a version of usher_barcodes.feather and lineage_mutations.json that didn't include BA.3..2.1 and BA.3.2.2.
I upgraded to Freyja 2.0.1 (I was still working on the 1.5.3 version), but the freyja update command made me download a version that didn't have it either... I ended up download directly those 2 files, as there was no issue with the other files. One of my colleagues tried himself too and had the same issue. Am I the only one with this issue?

[joshuailevy]

Oh, I think you may just need to update your barcodes - the 2.0.1 release comes with older barcodes, but they can be easily updated to the most recent barcodes using the freyja update command.

The most up to date barcodes do include both BA.3.2.1 and BA.3.2.2. https://github.com/andersen-lab/Freyja/blob/main/freyja/data/lineage_mutations.json

[mariemoinet]

sorry, that's what I meant. freyja update, not freyja upgrade. Somehow the cron job that I have set up seems to have fetched the latest version without problem. I guess this issue can be closed for now.

EDIT: I was wondering how the problem had been solved one week and reappeared the next week (my cron job runs weekly)... the problem hadn't disappeared, it's just that a colleague had downloaded the files from the github repo after I had mentioned the issue and had forgotten to let me know...

[joshuailevy]

ok, great! Thanks for the update @mariemoinet!

[mariemoinet]

as a heads up @joshuailevy, the issue hasn't been solved. I however am going to create a new issue under Freyja rather than this repo, as it concerns the last version and not older versions of barcodes.

[joshuailevy]

Hi @mariemoinet - I just checked to make sure, the barcodes do include BA.3.2.1 and BA.3.2.2. Can you provide the commands you're using to update the barcodes so I can recreate the issue on my side?

[mariemoinet]

Hi @joshuailevy,
I just use
freyja update --buildlocal --outdir ${NEW_BC}
(NEW_BC being a local directory with the date)
it works with no obvious error, and I get all files I need...
but if, for instance on the last version downloaded this Monday (19/01/2026), I search for a recent lineage like RE.1.1.3,
it is listed in lineages.yml and curated_lineages.json,
but not in the lineage_mutations.json or usher_barcodes.feather files (in fact no parent lineage of RE.1.1.3 appear in those files except BA.3).
I quite obviously end up with analyses (wrongly) telling me I have BA.1 and BA.2 sequences.
the md5 sums for these 2 files are:
4df4fed4df5314f85ffc5b008e3f56d3 lineage_mutations.json
f4e8b4fe0c1489117f89c1d7da93e1a8 usher_barcodes.feather
The script running this command uses Freyja 2.0.1 from docker.
OS: Rocky Linux 8.10 (Green Obsidian) x86_64
My work around is to download these 2 files from this repo before starting my analyses, but it would be nice if the update command worked as expected... I suspect this issue may be linked to this other issue as it also involved a local database.

[joshuailevy]

HI @mariemoinet - oh, I didn't realize you were building the barcodes yourself, rather than taking the barcodes from the Freyja or Freyja-data repositories.

My immediate thought is that you may just be missing these lineages because they largely present only on GISAID, and not via public INSDC databases. The tree used by the --buildlocal command is the public tree by default, whereas for the barcodes used on Freyja/Freyja-data, we use the tree of all known sequences, public and private.