kraken table taxonomy rank not assigned correctly with kraken database k2_standard_20251015

[WeimingWHu]

We recently downloaded newer version of kraken database: k2_standard_20251015. But the output of all_samples.tsv taxonomy column is not assigned to the rank correctly. The Kingdom level is missing and has two phylum levels, the phylum level got assigned to the kingdom, but it did not happen for all phylum, only 4 of them from my dataset. I used sunbeam4.7.0, this worked fine with kraken database standard_20240605. The kraken extension used "summarize_kraken2_reports.py" to put together the taxonomy.

For example:
Bacillota; ; Clostridia; Lachnospirales; Lachnospiraceae; Roseburia; Roseburia intestinalis
Bacillota; ; Clostridia; Lachnospirales; Lachnospiraceae; Roseburia;