# Can we increase the percent identity threshold for metaplan when running humann3

**URL:** <https://forum.biobakery.org/t/can-we-increase-the-percent-identity-threshold-for-metaplan-when-running-humann3/2817>\
**Category:** HUMAnN\
**Created:** [November 20, 2021, 8:35am UTC](https://forum.biobakery.org/t/can-we-increase-the-percent-identity-threshold-for-metaplan-when-running-humann3/2817 "2021-11-20T08:35:53Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![eo24a](https://avatars.discourse-cdn.com/v4/letter/e/b9bd4f/32.png) [@eo24a](https://forum.biobakery.org/u/eo24a)\
**Post date:** [November 20, 2021, 8:35am UTC](https://forum.biobakery.org/t/can-we-increase-the-percent-identity-threshold-for-metaplan-when-running-humann3/2817/1 "2021-11-20T08:35:53Z")

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Hi,

I have simulated a metagenome sample from known species. When running humann3 for this metagenome sample, during metaphlan stage some reads are matching to a species that does not exist as an input. I bowtie2’ed the simulated reads against the species that matahplan output gives and there is 60-70% read match. I wonder if I can increase the percent identity threshold for metaphlan option when running humann3 so that the metagenomic reads will not match with other species.

Thank you for your help,

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**Author:** ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)\
**Post date:** [February 11, 2022, 9:50pm UTC](https://forum.biobakery.org/t/can-we-increase-the-percent-identity-threshold-for-metaplan-when-running-humann3/2817/2 "2022-02-11T21:50:55Z")

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Hello, When running HUMAnN you can provide any options you would like to set for MetaPhlAn by using the option `--metaphlan-options <option>`.

Thank you,  
Lauren