I have HUMANn 3.8 installed and wanted to recover a taxonomic and functional profile with our samples. After I am looking at the StrainPhlan tutorial and I need to provide these options within metaphlan
This worked partially since I got a SAMS folder an sam files but the BOWTIE2 folder is empty. An additional question would be "Can I use the bowtie files within the humann_temp folder to feed StrainPhlan?
You can pass additional options to MetaPhlAn via HUMAnN using the --metaphlan-options flag. However, I find it’s often easier to just run MetaPhlAn outside of HUMAnN (using whatever parameters you’d like), and then pass the resulting taxonomic profile to HUMAnN via its --taxonomic-profile flag. It turns into a two-step process per sample, but it makes it a little easier to control each step.
Thanks for your help, I am now trying to run both HUMAn 4 and MetaPhlAn 4 I installed both software in the same environment and maybe that made it difficult to setup the databases (I got an error similar to Humann database errors (a short novel) - #3 by RbccBstn). I am currently re-downloading the metaphlan database to make it work but I wanted to thank you for this reply above.
I was trying to run the pipeline using first metaphlan and then humann 4 alpha.
I installed diamond and also provided the route to the databases with humann_config
I haven’t exhaustively searched older threads but is there anything wrong with the procedure above? Or is there an alternate way to pass the metaphlan output to humann?
Thanks for the help,
Best,