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.
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 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?
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.
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
@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.