Kraken2 tool error

The datamanager working fine in my case now.

But unfortunately, I have received some error as following.(convert kraken)

line 9: taxonomy-reader: command not found

Need some suggestions to resolve

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@vmevada102 Also, what version of Galaxy are you running? The latest release 19.01? Or cloud or docker version (which/source)?

Quick troubleshooting: This looks like a dependency problem. You can check the status under the Admin menu for all installed tools.

Ok, was reviewing other post. The Kraken2 databases might not have been set up correctly (pending an update). Likely related to this:

In short, you’ll need to wait for the updated tool versions for the Kraken2 suite and/or consider using the older versions of the tools in the meantime. Development links for work-in-progress are included in that other thread.

I am using 19.01 version in local server.

There is no any issue found in dependency tools… All dependency installed properly

Thank you @jennaj

It is good tool to use in metagenomics analysis…

It will be beneficial if updated.

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Kraken2tax. Used to concert kraken taxonomy to view result in krona

But it is not working with kraken2 output file

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Full tool name:

Convert Kraken data to Galaxy taxonomy representation

You’ll need to use the same version of all the Kraken tools in the same analysis. This includes the Data Manager (that creates the associated indexes).

In short, avoid the Kraken2 version of all upstream tools until the DM is ready or problems can come up.

@dfornika I could be missing something here, or this is part of a work-in-progress, or known issue, or something we need to ticket. From what I can tell “Convert Kraken data to Galaxy taxonomy representation” (tool id “Kraken2tax”) only has one version in the ToolShed, and it is older (2017). It will access Kraken indexes. Not sure if it is expected to list both Kraken and Kraken2 indexes once the Kraken2 DM is finalized/used. Or, if there will be a new version of the tool for that functionality (one for Kraken, one for Kraken2). However done, the form(s) should point to the correct indexes based on the upstream tool version. The current short tool name is a bit confusing but not much can be done about that (“Kraken2tax” means “Kraken-TO-taxonomy”). Maybe there will be a Kraken22tax :smile: with a new tool name like “Convert Kraken2 data to Galaxy taxonomy representation” or some reorganization at the data table level for the existing Kraken2tax so that it captures all indexes?

Also pinged @dfornika at the IUC tool development forum here:

I’m not certain what the best solution will be, it might be possible to make kraken2tax compatible with both kraken and kraken2 output. Or, as @jennaj suggested it may be necessary to create a kraken22tax tool.

I noticed this issue on the tools-iuc repo where this can be discussed and followed more closely.

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Linked discussion: How to view Kraken2 Results in Krona?

Sorry I missed that at first!

I see that there is an datamangers for kraken2 to install Minikraken2. Now I am able to install Minikraken2 but it doent contain all the required files to finish the job.
taxo.k2d file is missing.

Fatal error: Exit code 2 ()

Possible unintended interpolation of @2 in string at /dep/_conda/envs/__kraken2@2.0.7_beta/bin/kraken2 line 16.

kraken2: database ("/tool/tool-data/kraken2_databases/2019-05-07T122927Z_minikraken2_v2_8GB") does not contain necessary file taxo.k2d



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Thanks, I’ll add this information to the Github ticket above.

The Kraken2 Data Manager needs some tuning.

Update (new Kraken2 DM released today): Database indexes for Kraken and Kraken2

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@jennaj Apologies for a simple issue but, I am unable to link a fasta output from Plasflow (or any fasta producing tool) to Kraken2 in Workflow mode (i.e. drag the arrow from the Plasflow output to Kraken2 input), however, I can analyze fasta files via Kraken2 in the interactive/Analyze Data mode.

As I have a set of samples I would like to use the Workflow mode. I figure it is a simple missed flag in the underlying code for Kraken2.