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

[ingridvanw]

@davv2
I hope you can comment on this :)?
Thanks in advance!

[davve2]

Hi Ingrid,

sorry for a delayed response. Flextaxd is not really doing any selection on assembly level, what may cause the issue is that when annotating the genomes with nucl_gb it doesn´t include the correct annotation for the sequence in question. To ensure all sequences being annotated from NCBI I recommend to download and merge nucl_gb.accession2taxid.gz with nucl_wgs.accession2taxid.gz

You can find a description on how to do that here https://github.com/FOI-Bioinformatics/flextaxd/wiki/8d.-Walkthrough--merge-NCBI-and-GTDB under section 1.2

Let me know if this is not solving your problem and I will try to look into it.

Kind regards,
David

[DariaOGajewska]

Hi,

I encountered a similar problem. I have a genome dataset of about 20k sequences and after "cleaning", 4k sequences of it were removed. After that kraken2 database was created from a flaxtaxd file the database weighs about 50GB.

Then I tried David's method to concatenate the "nucl_gb.accession2taxid" and "nucl_wgs.accession2taxid". I build the database with "flextaxd-create" exactly the same as before but with a new accession2taxid, I drastically ran out of storage space, and it was around 700GB.

Is this extreme increase in storage usage expected during the database-building process with a concatenated accession2taxid file?

Any insights or suggestions would be greatly appreciated!

Kind regards,
Daria