kraken-biom empty .biom files from normal-looking bracken reports?

hi

Im trying to make .biom files from three sets of reports, 1 from kraken2 and 2 from bracken. The kraken2 and first bracken work fine (theyre both down to species level, and i use --fmt json and give a -o FILE NAME). the second bracken collection (i set the level at genus when running bracken here) gives an empty .biom file.

to show what is going on, this is a "normal" .biom file:

head brackenTry_S.biom {"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by": "kraken-biom v1.0.1 (http://github.com/smdabdoub/kraken-biom)","date": "2022-06-20T16:05:23.802520","matrix_element_type": "float","shape": [187, 5],"type": "OTU table","matrix_type": "sparse","data": [[0,0,18139.0],[0,1,152.0],[0,2,14961.0],[0,3,11830.0],[0,4,2683.0],[1,0,9957.0],[1,1,112.0],[1,2,6612.0],[1,3,17086.0],[1,4,12027.0],[2,0,8659.0],[2,1,169.0],[2,2,96.0],[2,3,3599.0],[2,4,119.0],[3,0,891.0],[3,1,177.0],[3,2,2879.0],[3,3,1999.0],[3,4,2521.0],[4,0,746.0],[4,1,858.0],[4,2,477.0],[4,3,228.0],[4,4,219.0],[5,0,386.0],[5,1,96.0],[5,2,257.0],[5,3,1494.0],[5,4,211.0],[6,0,59.0],[6,1,13.0],[6,2,180.0],[6,3,170.0],[6,4,63.0],[7,0,27.0],[7,1,38.0],[7,2,346.0],[7,3,230.0],[8,0,195.0],[8,1,41.0],[8,2,1028.0],[8,3,393.0],[8,4,586.0],[9,0,115.0],[9,2,231.0],[9,3,98.0],[9,4,83.0],[10,0,40.0],[10,2,100.0],

this is the "empty" .biom file:

head brackenTry_G.biom {"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by": "kraken-biom v1.0.1 (http://github.com/smdabdoub/kraken-biom)","date": "2022-06-21T08:48:03.724794","matrix_element_type": "int","shape": [0, 0],"type": "OTU table","matrix_type": "sparse","data": [],"rows": [],"columns": []}

also, when trying to import the "empty" .biom file in phyloseq (R-studio):

> brackenGenuses <- import_biom("brackenTry_G.biom") Error in h(simpleError(msg, call)) : error in evaluating the argument 'object' in selecting a method for function 'otu_table': 'names' attribute [3] must be the same length as the vector [0]

Not sure what happens here. I've inspected all the original kraken2 and bracken report files and there seem to be no issue here, can post examples if needed. Any ideas?

many thanks Martin