how to use multiple databases and generate krona.html and bubbles.svg?

[AravindPattisapu]

Hi, I have been using kaiju recently and want to use the virus, plasmids and fungi databases from here: https://kaiju.binf.ku.dk/server

I downloaded the databases .tgz files and put each kaiju_db_*.fmi, nodes.dmp, and names.dmp files into the kaiju/bin folder.

For a single db, I ran ./kaiju -t nodes.dmp -f kaiju_db_viruses.fmi -i SRR12180973_2.fastq -o run1.out

And also followed the other steps to generate the krona.html file. It worked.

But for multiple dbs, the problem is that the nodes.dmp and names.dmp files have the same name for each of virus, plasmids and fungi, so I tried adding suffix like nodes_viruses.dmp and names_viruses.dmp, and also changed the command to:

./kaiju -t nodes_*.dmp -f kaiju_db_viruses.fmi -i SRR12180973_2.fastq -o run1.out'

But the output file doesn't show the results from all dbs, only one.

I also tried concatenating the multiple nodes.dmp and names.dmp files into a single one, but still the output krona file only shows results from one db.

How to get a krona.html and bubbles.svg output file like they provide on the binf result page?

Please let me know if you fail to undestand any of my problems

[pmenzel]

Just extract the various tgz files that you downloaded into separate folders. Note that you can run kaiju with only one DB at a time for a input fastq file. You can use the kaiju-mergeOutputs program to merge multiple output files into one and use that as input for kaiju2krona.