Running alpha diversity on combined bracken reports

[adixit213]

I ran bracken on the PlusPFP and a custom database.Combined the .bracken outputs from both using combine_bracken_outputs.py.
So far so good. When I ran the alpha diversity on the combined bracken output and redirected the output to a file, its only showing the alpha diversity value for the custom database. Not sure why that would be the case. Verified that the .bracken reports were in fact combined and there is information pertaining to both mappings (PlusPFP and custom). Any help/advice will be great.
Thank you.
Here is my two lines of code.
python combine_bracken_outputs.py --files PlusPFP.bracken Custom_database.bracken --output Combined.bracken
python alpha_diversity.py -f Combined.bracken -a Sh > Alpha_Diversity.txt