HUMAnN 4.0.0.alpha.1 calls "old" metaphlan command-line args

[seandavi]

When running HUMAnN 4.0.0.alpha.1 in combination with metaphlan4.2, I get this error:

metaphlan: error: unrecognized arguments: --bowtie2out /scratch/local/15180086/work/65/d80912c037b7b57fc0ff8e00db797b/out_humann_temp/out_metaphlan_bowtie2.txt

Probably expected given the changes to metaphlan4.2 command-line arguments, but it leads to being unable to run humann on a new sample directly.

[franzosa]

Confirmed, the next version of HUMAnN will address this, including adding broader support for MetaPhlAn 4.2 + the updated Jan25 SGB set. In the meantime please see here for workarounds:

Humann 4 cant work with metaphlan 4

We will be adding support for MetaPhlAn 4.2 + the Jan25 SGBs in the next release of HUMAnN. Right now the HUMAnN 4 alpha does not yet support these latest versions. My recommendation would be to stick with running HUMAnN 4 with MetaPhlAn 4.1 + the Oct22 SGBs for now. If you’d like to also experiment with MetaPhlAn 4.2, you could do so in a separate conda environment. If you would like to use MetaPhlAn 4.2 output with HUMAnN, you could run MetaPhlAn outside of HUMAnN including the following flag…