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I have quite a few results in my tree that are "unassigned Eukaryota (13)" or "unassigned Plasmodium (1168)" for instance. How should I interpret this?

Keanu fails to correctly locate the deepest common classification in cases where a contig has BLAST hits to multiple sub-categories of root as described here. For example, if a contig has an alignment to cellular organisms and to Viruses, then Keanu fails to correctly assign the contig to root.

https://github.com/pbuendia/keanukraken

Running the following results in all reads being assigned to the root node only.

python3 keanu.py -db taxonomy.dat -md_db merged_deleted.dat -in test.txt  -view tree -out output/sample.tree.html

Input file:

read1   1176533 [1]
read2   9606 [1]
read3   1308 [1]
read4   724 [1]
read5   9606 [1]
read6   9606 [1]
read7   9606 [1]
read8   1236 [1]
read9   158836 [1]
read10  39694 [1]

Running the same command but with the following input yields the expected results. The new input file just adds column 2 to itself (i.e. awk "{$2 = $2 ', ' $2} 1")

read1   1176533 [1], 1176533 [1]
read2   9606 [1], 9606 [1]
read3   1308 [1], 1308 [1]
read4   724 [1], 724 [1]
read5   9606 [1], 9606 [1]
read6   9606 [1], 9606 [1]
read7   9606 [1], 9606 [1]
read8   1236 [1], 1236 [1]
read9   158836 [1], 158836 [1]
read10  39694 [1], 39694 [1]

In some cases, such as cases where the only common classification is root, users may be interested in simply viewing all the data, rather than viewing Keanu's more certain but less defined assignments.