Humann3 zero species selected from prescreen

Hello, I am running humann3 on a metatranscriptome sample from a lake. In the sample, I am expecting lots of algae and bacterial species. However, when I run humman3, I get zero species selected and 92% unaligned reads.
Is there a reason why zero species are selected in the metaphlan prescreen? Thanks for your help!

Below is my output:

Running metaphlan …

Total species selected from prescreen: 0

Selected species explain 0.00% of predicted community composition

No species were selected from the prescreen.
Because of this the custom ChocoPhlAn database is empty.
This will result in zero species-specific gene families and pathways.

Running diamond …

Aligning to reference database: uniref90_201901b_full.dmnd

Total bugs after translated alignment: 1
unclassified: 261886 hits

Total gene families after translated alignment: 3892

Unaligned reads after translated alignment: 92.0665000000 %

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I’m getting the same problem. If you solved the problem, how did you solve the problem?


I got the same problem too!!! Even with the demo files. It seems that might be a problem of humann3 rather than the dataset!

I’m facing the same issue as well. can anyone please assist me in this matter? I’m using shotgun sequences. Thanks!

Hello, The HUMAnN output folder contains the taxonomic profile generated by MetaPhlAn. If you would check out this file to see if it identifies any species and if so note their abundance levels. It might be possible there is an error running MetaPhlAn, or MetaPhlAn does not identify any species, or the species identified are less then the default abundance prescreen threshold in HUMAnN (so they are all filtered).

Feel free to post here with more info if needed to follow up.