Metatranscriptome workflow, with more than one metagenome

Hi, I have five metatranscriptome samples, which correspond four metagenome samples. I previously assembled the metagenome samples into contigs, to which the metatranscriptome samples were mapped (with bowtie2), and used the resulting .sam of each sample to run HUMAnN. However the results only said ‘UNMAPPED’ and ‘UNINTEGRATED’ . I think it’s because the taxonomic information was not included.

So on the main page of github, I saw that you suggested to first analyse the metagenomes and then use the result in the --taxonomic-profile flag of metatranscriptome samples. Since I have more than one metagenome, is it possible to run HUMAnN with the contigs.fasta? Or if I have to run each sample separately, would it make sense to compile the taxonomic profiles into a single file, to later use for all metatranscriptome samples?

Thank you,