100% no hits

[dbu008]

Dear All,

I searched for a solution here but I could not find it. I feel my problem would be very simple, however, I am just starting to use the Krona.

I installed Krona as an easybuild. I am running Krona on HPC.

First, I used Kraken2 and Centrifuge for the taxonomic classifications, cut the columns that I want to displayed in Krona. Then, after installation and the use of updateTaxonomy.sh I run Krona like here:

`./ImportTaxonomy.pl /cluster/bla/bla_unclass.krona -o /cluster/bla/bla//Kraken2/DIR_01.krona.html

Loading taxonomy... Importing /cluster/bla/bla_unclass.krona... Writing /cluster/bla/bla//Kraken2/DIR_01.krona.html...

[ WARNING ] Too many query IDs to store in chart; storing supplemental files in '/cluster/bla/bla//Kraken2/DIR_01.krona.html...'.`

I enclosed the example of my input file and output file. In the output *.html there is 100% no hits. This is not true, as you will see I have a lot of hits.

exa.txt

I would be glad if someone could explain and help me how to run to get my input displayed by Krona.

Best regards, Dorota

[conchaeloko]

Hi Dorota,

I actually have the same issue, did you manage to solve it ? Best, Robby

[levinyi]

do not use --use-names when using kraken2,

that works for me.

kraken2 --db /path/to/kraken2_database   --report ./sample.raken2.report --output ./sample.kraken2.output /sample.fastq
le  ./sample.kraken2.output |cut -f 2,3 >sample.kraken.krona
ktImportTaxonomy sample.kraken.krona

Although still warning, the graph is correct!

[omrctnr]

I think the problem is that you should have used kraken's report. exa.txt is output of kraken.

Please check it: https://github.com/DerrickWood/kraken2/wiki/Manual#sample-report-output-format

[varundeepakgudhe]

Hi, I generated kraken outputs the output file and report file and I used ktImportTaxonomy to generate html files but I am getting 100% no hits. Can I please know why? ktImportTaxonomy B205.kraken -o B205.kraken.html