# Metaphlan 4 database during humann3 run

**URL:** <https://forum.biobakery.org/t/metaphlan-4-database-during-humann3-run/6875>\
**Category:** MetaPhlAn\
**Created:** [April 1, 2024, 7:16am UTC](https://forum.biobakery.org/t/metaphlan-4-database-during-humann3-run/6875 "2024-04-01T07:16:26Z")\
**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:** [April 1, 2024, 7:16am UTC](https://forum.biobakery.org/t/metaphlan-4-database-during-humann3-run/6875/1 "2024-04-01T07:16:26Z")

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Hi,

I have tried metaphlan --install to download the databases, it did not work properly. So I have downloaded them using wget option. the indexes, bt2.tar and bt2.md5 and mpa\_vJun23\_CHOCOPhlAnSGB\_202307.tar and md5 files. I downloaded them outside of miniconda3 to my own folder.

Then, when I ran humann3: this is my code.

path/to/humann --input fastq.gz --protein-database path/to/humann3\_databases/uniref --threads 16 --search-mode uniref50 --nucleotide-database path/to/humann3\_databases/chocophlan --bowtie2 path/to/miniconda3/bin/ --metaphlan-options “–bowtie2db path/to/metaphlan\_databases/” --metaphlan-options “–index path/to/metaphlan\_databases/mpa\_vJun23\_CHOCOPhlAnSGB\_202307” --output X\_uniref50.trimmed\_humann3

it deletes all the md5 and tar files from the database folder. why does it deletes the files from the database folder. Then, I need to redownload them everytime I ran humann with a new input. Do I need to re-download them each time I ran humann? How I can solve this issue?

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**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\
**Post date:** [April 11, 2024, 6:28pm UTC](https://forum.biobakery.org/t/metaphlan-4-database-during-humann3-run/6875/2 "2024-04-11T18:28:30Z")

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I’m going to move this over to the MetaPhlAn channel since I don’t think this is something that HUMAnN specifically is doing. I can confirm that you do not need to redownload anything for MetaPhlAn each time you want to run HUMAnN.