Taxonomy IDs not matching

[AmaliT]

Hi @jenniferlu717

Thanks for great tool. I am trialling the bracken tool on the kreports generated from kraken2. Braken run completed successfully, however when I was trying to use the combine_bracken_outputs.py script I get the following error: "Taxonomy IDs not matching for species Senegalia: (1924097 468156)". When I checked for the genus on taxonomy DB on NCBI, it seems there is two of these - one in the plant world and the other in bacteria. So I was wondering how do I get around this duplicate issue? Any suggestions?

Thanks in advance

Cheers Amali

[HitMonk]

Hello I was wondering if anone had solved this issue? I too have the same problem only when using the SILVA database. Both the RDP and GG seem to work fine. I get the same taxonomy IDs not matching error:

python2.6 /project/umb_rick_kesseli/Nachi/apps/Bracken/analysis_scripts/combine_bracken_outputs.py --files Silva/Gen1-160_191.bout Silva/Gen1-163_215.bout Silva/Gen1-27_138.bout -o trial.silva PROGRAM START TIME: 01-12-2021 11:01:27 Processing Output File Silva/Gen1-160_191.bout:: Sample Gen1-160_191.bout Taxonomy IDs not matching for species uncultured: (46400 46232)

[timregan]

I have the exact same issue. Also using SILVA. Any solutions a year on?

python ../bracken_combine_outputs.py --files *genus.bracken -o bracken_genus_all PROGRAM START TIME: 06-11-2021 10:51:38 Processing Output File 7_T12_Trip1A.kreport2.report.genus.bracken:: Sample 7_T12_Trip1A.kreport2.report.genus.bracken Taxonomy IDs not matching for species uncultured: (26127 2666)

UPDATE: I fixed this by removing all lines with "uncultured" in them as this was the Taxa throwing the error. Probably better to collapse these lines rather than remove them but it works for now.

[susheelbhanu]

I can confirm that @timregan's suggested method works!