# \--nucleotide-identity-threshold does not change run config or results (humann v3.8)

**URL:** https://forum.biobakery.org/t/nucleotide-identity-threshold-does-not-change-run-config-or-results-humann-v3-8/9003
**Category:** HUMAnN
**Created:** [July 17, 2026, 8:16pm UTC](https://forum.biobakery.org/t/nucleotide-identity-threshold-does-not-change-run-config-or-results-humann-v3-8/9003 "2026-07-17T20:16:50Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![Gsmith535](https://avatars.discourse-cdn.com/v4/letter/g/85f322/32.png) [@Gsmith535](https://forum.biobakery.org/u/Gsmith535)
#### Post date: [July 17, 2026, 8:16pm UTC](https://forum.biobakery.org/t/nucleotide-identity-threshold-does-not-change-run-config-or-results-humann-v3-8/9003/1 "2026-07-17T20:16:50Z")

</div>

I want to look at variations of read identity, as a high-level proxy for population variation, on human microbiome sample profiling using humann v 3.8 (i have been unable to install more recent versions).

There is an obvious parameter to set, --nucleotide-identity-threshold.

However, there is no apparent alteration to the run config regarding nucleotide identity thresholds.

```auto
humann -i reads.fq -o humann_default --output-basename default --threads 10 --taxonomic-profile metaphlan.txt
grep 'nucleotide identity threshold' humann_default/humann_default_humann_temp/humann_default.log
nucleotide identity threshold = 0.0

humann -i reads.fq -o humann_90nuclid --output-basename default --threads 10 --taxonomic-profile metaphlan.txt --nucleotide-identity-threshold 90
grep 'nucleotide identity threshold' humann_90nuclid/humann_90nuclid_humann_temp/humann_90nuclid.log
nucleotide identity threshold = 0.0

```

The resulting outputs also suggest that the parameter did not affect the run - abundances of gene families are exactly identical across all \>600K gene families with taxonomic information.

As there are newer versions of the tool, i don’t expect a fix to the version I am using. But please check v4.