Question about assembly level in creating flextaxd database

[ingridvanw]

Hi guys,

Thank you for developing this tool.

I have one question. I downloaded genomes with all types of assembly from NBCI (Refseq).
When created the flextaxd database, I noticed in the inspect.txt file that genomes with assembly level contig are not in there.
It is possible to create a flextaxd database with genomes with assembly-level 'contig'? (Of is the 'minimum level' scaffold?)

Commandlines I have used
datasets download genome taxon --assembly-source RefSeq --assembly-level chromosome,complete,scaffold,contig Mycolicibacillus --filename mycolicibacillus.zip
--> download 7 genomes

flextaxd --db mycolicibacillus.fdb --taxonomy_file nodes.dmp --taxonomy_type NCBI --genomeid2taxid nucl_gb.accession2taxid.gz --genomes_path genomes

flextaxd --db mycolicibacillus.fdb --clean_database --taxonomy_type NCBI

flextaxd-create --db mycolicibacillus.fdb --genomes_path genomes --dbprogram kraken2 --create_db --db_name kraken2.mycolicibacillus --processes 20
--> mycolicibacillus trivialis is not in inspect.txt (GCF_002102395.1)

Thanks in advance!
Kind regards
Ingrid