I’ve recently upgraded to humann v3.9 & MetaPhlAn version 4.2.2 and it appears that the way MetaPhlAn handles map files has changed, so the ‘–bowtie2out’ arg is now ‘–mapout’ (as mentioned in the release announcement)
An example PR at Update for MetaPhlAn 4.2 compatability by zzkt · Pull Request #67 · biobakery/humann · GitHub
The same issue is present in HUMAnN 4.0.0a1
I also am having compatibility issues with HUMAnN v4.0.0.alpha.1 and MetaPhlAn 4.2.2 as a result of --bowtie2out no longer being an arguement. Any suggestions on how to address this?
You can try patching a local copy of HUMAnN to use the new arg prefix (specifics here). It should still pass all the tests run by humann_test and humann_test --run-functional-tests-tools.
Seems to work as expected so far…