No pseudogenes being detected

[flashton2003]

Hi Oliver,

We are interested in pseudogenes in a Salmonella genome. My colleague has run bakta, but no pseudogenes are being detected. This is unexpected based on some other analyses we have carried out, but I haven't been able to identify any specific discrepancies (the other analysis is a random forest, and I haven't unpicked it yet).

Bakta was installed via conda. The bakta output directory can be downloaded from here as a dropbox link.

https://www.dropbox.com/scl/fo/3ml720rn2clv2f68sc2qm/AHrkm3NUddod6KWhQRggpJw?rlkey=m7vl1loes8ij9ppny2zm29ubu&dl=0

Any thoughts?

Thanks,

Phil

[oschwengers]

Hi Phil, based on the logs the light db version was used. For the pseudogene detection, however, Bakta requires the full db version. Maybe I just add a line to STDOUT to clearly express this behavior.

Best regards!

[flashton2003]

Great, thanks Oliver!

On Thu, 12 Sep 2024 at 16:55, Oliver Schwengers @.***> wrote:

Hi Phil, based on the logs the light db version was used. For the pseudogene detection, however, Bakta requires the full db version. Maybe I just add a line to STDOUT to clearly express this behavior.

Best regards!

— Reply to this email directly, view it on GitHub https://github.com/oschwengers/bakta/issues/320#issuecomment-2346531221, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAT6FEVAMUKSAZICXENTJ6TZWGTNHAVCNFSM6AAAAABN6X44U6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBWGUZTCMRSGE . You are receiving this because you authored the thread.Message ID: @.***>

[oschwengers]

FYI: the upcoming v1.10.0 will print a short note to STDOUT -> https://github.com/oschwengers/bakta/commit/c8a93e11cae31db58eab3711ca344e3ceaf35eba

Thanks for reaching out/reporting!