“Krakentools: Combine multiple Kraken reports” consistently fails with Kraken2 reports, irrespective of the number of reports. The relevant output is attached:
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Welcome, @Doron_Goldberg
To prepare the data for input to this tool, there is an intermediate tool named Kraken-report. It accepts raw Kraken classification results and outputs a report.
This shared history has an example using sample data from one of the GTN’s tutorials. You can import it and explore since you’ll have your own copy → https://usegalaxy.eu/u/jenj/h/example-for-krakentools-combine
Please also note that the tool you are using is only available for Kraken and not Kraken2. The tool name is similar but a lot changed between the releases in terms of data formats – so choose one and stick with it throughout a particular analysis path. Meaning, you can certainly run both on your data, but avoid mixing up the files or you’ll have potential problems (not just tool errors, but content issues).
If you are not following a metagenomics tutorial yet, try scrolling down to the bottom of the Kraken or Kraken2 tool forms. These will explain common data summary options. Even if the data in those full analysis examples are not exactly your goals these are usually helpful.
Hope this helps! 
Jenna Hi,
Thank you for your kind reply. I have followed the tutorial step by step. However, when I switched to Kraken instead of Kraken2, I found that there was no database suitable for plants. I have sequences produced by Oxford Nanopore of the ITS region of pollen grains, which need to be sorted according to their species.
Thanks again,
Doron
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I did some extra checking, and it seems that the Kraken2 → Krakentools: Kraken-report tool should work!
We have a tutorial that includes that process here → Hands-on: Identification of the micro-organisms in a beer using Nanopore sequencing / Identification of the micro-organisms in a beer using Nanopore sequencing / Microbiome
And I started up a test using the tutorial’s data and workflow in a shared history here → https://usegalaxy.eu/u/jenj/h/test-beer-data-analysis
That is still running. This is testing the first step: generating a “report” format from Krakentools. The next step is combining those custom reports.
Now, I don’t know if that downstream Krakentools: Combine tool will work on those report outputs or not, but that is something you could explore.
Either way, we would be interested in the result!