Database issues with humann3 and metaphlan

Microbial community profiling MetaPhlAn
1

Dear all,
I got an error when I tried to run the following command:
humann --input-format fastq --input out.unmap.fastq --output ./ --threads 40 --search-mode uniref90

截屏2025-02-13 09.00.45
截屏2025-02-13 09.00.452642×748 64.9 KB

I can guarantee that there is no problem with the fastq file, because I created a new, very small fastq file, and the same problem still occurs.
The versions I used are humann v3.9 and metaphlan v4.0.6

2

I’m moving this thread from HUMAnN to MetaPhlAn since the error seems to be arising from the MetaPhlAn run itself. This does look as though the error is arising from the nreads count being zero, which could arise as a result of a poorly formed input, but if you’re 100% sure that’s not the case then it could be something more subtle.