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

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.

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: