Set --identity-threshold as 50

Hello, the version of HUMAnN is 2.8.2. The default parameter of --identity-threshold depends on the search mode, Uniref 50 or Uniref 90.

I want to use the intermediate files where --search-mode is set as Uniref 90 and --identity-threshold is 90.0 to re-analyse the data at the identity threshold of 50.0.

humann2 -r -o humann2/ --nucleotide-database database/index --protein-database protein/ --threads 10 -i clean.fastq --identity-threshold 50.0

But the log file shows the identity threshold is still 90.0.

Therefore, is it feasible to set the --identity-threshold as 50.0 under Uniref 90 search mode.

Thanks in advance!


There is a feature/bug in HUMAnN 2.x that prevents “accidentally” using 50% ID when working with a UniRef90 database. As a workaround you can set it the ID threshold to something like 50.000001% and it should work as expected.