it has this same error with providing it a reference database instead of having it find one. Issue is

eukulele/gtdb/reference.pep.fa: No such file or directory
eukulele/gtdb/taxonomy-table.txt: No such file or directory

this is what is in the GTDB path

FILE_DESCRIPTIONS  RELEASE_NOTES            ar122_r202.tree          bac120_metadata_r202.tsv  genomic_files_all
MD5SUM             VERSION                  ar122_taxonomy_r202.tsv  bac120_r202.tree          genomic_files_reps
METHODS            ar122_metadata_r202.tsv  auxillary_files          bac120_taxonomy_r202.tsv

so not seeing the files it is requesting, but I redownloaded the db and they definitely are not there (not sure why it's looking for these when they don't come with the DB unless it generates them?)

Hi!

eukulele

works by using certain files and tables like

reference.pep.fa

and

taxonomy-table.txt

those can be: a. downloaded directly by

eukulele

b. provided by the user c. created by using

create-protein-table.py

script provided by

eukulele

Unfortunately for GTDB is not downloaded automatically from this

eukulele

version (it's a feature that we hope to see in a future release) therefore you will need to create the database by following the instruction here: https://eukulele.readthedocs.io/en/latest/databaseandconfig.html or choosing another database at the moment.