Problem with Taxonomy Database -- Use the Kraken Data Manager to install indexes

[vmevada102]

Dear galaxy community

I am trying to run the Kraken for metagenomics data. it works very nicely.

Unfortunately at the last stage of the kraken. kraken to galaxy taxonomy, the reference database was not found.

As per the previous solutions listed in the Community, I had installed the gb_taxonomy tool. But still could not setup the databsse for taxonomy conversion to view in Kraken results in Krona.

Please suggest how to solve the datbase solution.

[vmevada102]

Waiting for reply community. Need some suggesstions

[jennaj]

Hi @vmevada102!

Have you installed the Kraken Data Manager and run it to create the indexes used by the tool? I’m not sure if this DM requires a restart or not, so if after install the indexes still cannot be found, try doing that.

The Galaxy ToolShed has two versions. Use the one that matches the version/author of the other tools already installed.

• data_manager_build_kraken2_database Contains data managers that define and populate the kraken2_databases tool data table.

• data_manager_build_kraken_database Contains a data manager that defines and populates the kraken_databases tool data table.

Thanks!

[jennaj]

Cross-linked Q&A:

How to view Kraken2 Results in Krona?

Hello all, I am working in the community analysis of the metagenomics data. Kraken2 is complied and merge all its previous separate tools to run in Galaxy. The problem i am facing is that, it will not generate file to view results in the Krona Pie chart. It is most essential step to visualize the results. kindly suggest some solution or update for the above said problem.

[vmevada102]

This tools were downloading the Database for the kraken2/kraken tool.

It is not downloading the taxonomy database for the Convert Kraken tool.

How to download the taxonomy database to work with Kraken2tax

[jennaj]

Please see the linked thread for the latest reply