Can I use humann3 database for humann2?

Microbial community profiling HUMAnN
1

Hi, I’m using humann2 docker latest version(2.8.0).
I’m trying to use humann3, but I noticed it is just in alpha version.

When I checked all databases used in humman, humann3’s database is x5 or more bigger than humann2’s. In my think, using updated, with bigger data, will lower unmapped reads.

So, Can I use humann3 database for humann2?
Thanks,

2

Hi - If you want to run with the HUMAnN v3 database also use the HUMAnN v3 software so everything is in sync. If you would like to use docker you can use the biobakery/humann image from dockerhub which contains the v3 software. Yes we currently have it tagged as an alpha version but we have finished our internal evaluations so please use the v3 version if you would like.

Thank you,
Lauren

1 Like
3

Thanks for your comment Lauren!

I’m trying to use humann3 docker version since last week, but I think I have a problem with metaphlan3 database installing.

When I run ‘metaphlan --install --bowtie2db’, it says ‘MD5 checksums do not correspond!’…
Can I get any help about this problem?
I searched the dropbox and downloaded mpa_v30_CHOCOPhlAn_201901.tar and mpa_v30_CHOCOPhlAn_201901.md5 from it , but it doesn’t work too.

Thank you,
minho

4

Hello - Try removing all of the files from the metaphlan_databases folder and then run the install. I think you should have enough space in the docker container to just use the default folder so you can run “$ metaphlan --install”.

Thank you,
Lauren

5

Thanks, Lauren,

I removed all the files in the location of ‘/usr/local/lib/python3.6/dist-packages/metaphlan/metaphlan_databases/’ and run metaphlan --install.
Now humann3 workes well on demo.fastq!

I’m using biobakery/humann:latest version from dockerhub. Thanks!

Thank you,
minho