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: https://genomics.sschmeier.com/ngs-taxonomic-investigation/index.html 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 updateTaxonomy.sh 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 "updateTaxonomy.sh" multiple times already and it does not change anything...
Any help would be much appreciated!