I am trying to create a krakenhll custom database using my own assemblies of strains within the same species. I am using this for all strain:
./krakenhll-build --add-to-library strain1.fa --db strain_db
./krakenhll-build --build --threads 40 -db strain_db
My problem is that in order to use '--add-to-library' I need to add taxid ID information which classifies them all as the same species and therefore all of the reads under the same name. On krakenhll's github it mentions being able to use:
krakenhll-build --generate-taxonomy-ids-for-sequences ...
"to add pseudo-taxonomy IDs for each sequence header." but this command does not appear to work, and within the help section I have tried using the recommended "--taxids-for-genomes' but this also appears to change nothing. Does anyone know how to label each input genome differently with or without using taxid IDs?