Adding new taxa to a Kraken2 db
Entering edit mode
7 weeks ago
valentinavan ▴ 20

Hi, can someone please check if these following steps are correct?

I am trying to add to my plants kraken2 db ("plant_original") few taxa genomes that I have downloaded from the NCBI website (alnus_glutinosa_GCA_003254965.1.fna, carpinus_fangiana_GCA_006937295.1.fna etc..).

for file in *.fna   
        kraken2-build --add-to-library $file --db PATH/kraken/plant_original

Masking low-complexity regions of new file... done. Added "alnus_glutinosa_GCA_003254965.1.fna" to library (PATH/kraken/plant_original)

Masking low-complexity regions of new file... done.

Added "carpinus_fangiana_GCA_006937295.1.fna" to library (PATH/kraken/plant_original)

Masking low-complexity regions of new file... done.

kraken2-build --build --db ~/kraken/plant_original

Creating sequence ID to taxonomy ID map (step 1)...

Sequence ID to taxonomy ID map already present, skipping map creation.

Estimating required capacity (step 2)...

Estimated hash table requirement: 73390180936 bytes Capacity estimation complete. [1h53m11.000s]

Building database files (step 3)... Hash table already present, skipping database file build. Database construction complete. [Total: 1h53m11.000s]

Then, I run kraken with one of my sample against this new updated plants db (I did not change the name of the db, is still called plant_original):

kraken2 --db PATH/kraken/plant_original --threads 8 --confidence 0.1 --report PATH/SB0new_report.txt PATH/SB0.fastq.gz --report-zero-counts --output PATH/SB0new_taxa.txt

However, the new kraken2 report is exactly the same as the old one and it did not find any hit to these new added taxa.

Previously, I did a blastn alignment of these sample’s reads with these exact same taxa (I created a small db with alnus_glutinosa_GCA_003254965.1.fna, carpinus_fangiana_GCA_006937295.1.fna etc..) and blastn could find some hits. So I was expecting that Kraken2 would have found these matches too.

Are these steps wrong or am I making some conceptual mistake?

I appreciate your help.


plants database blast kraken2 • 442 views
Entering edit mode
6 weeks ago
Mark ★ 1.1k

You can not add genomes to an existing, precomputed kraken db. You have to download the plant genomes, add the new genomes then recreate the db.

Entering edit mode

Hi Mark,

thanks for replying. Is it not what I have done? I have downloaded the genomes and added them to the db. Can you please be more specific so that I can understand. Thanks

Entering edit mode

Edit: Mark is right. You added new files to an existing library. Do you have the fasta files of the initial plant database?

Entering edit mode


Thanks for your help. I made custom database (from scratches), I tested Kraken2 with a sample and I got matches, however, when I created the db it also produced an unmapped.txt file with a long list of accession numbers. I am not sure how to treat this...

Please see this other post: Custom Kraken2 db


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