Kraken2 output visualisation with Krona Viruses not shown

Kraken2 output visualisation with Krona Viruses not shown


Dear all,
I am trying to visualize my kraken2 output with Krona and the results look very doubtful. I build a metagenomic pipeline with multiple filtering steps and I should have mainly viral sequences (a brief look into my kraken2 output files confirms this). However the Krona output displays around 50% bacteria and 50% “other root”.
I am sure this is a very silly mistake on my part somewhere but I cannot figure it out…
I used this guide: to install and run Krona and on the surface it seems to work but the output is definitely wrong.
Here is an example of my command when running:

$ ktImportTaxonomy file_kraken2_output.txt
Loading taxonomy…
Importing 20398_20_S19_combined_kraken2_output_report.txt…
[ WARNING ] The following taxonomy IDs were not found in the local database and were set to root (if they were recently added to NCBI, use to update the local
database): 588374 2572 990749 3 539464 36 588380 588378 169 377 26 8 15 4 130 29676 208 73 401669 12 5 135 390
Writing taxonomy.krona.html…<

I have run “” multiple times already and it does not change anything…

Any help would be much appreciated!

Here is an example of the output I get






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