Metaphlan results as input on Humann

Hi dears,
For some reasons, all my metagenome data had generated firstly by Metaphlan and now I want to run with humann. I browsed forum and found some related topics like:

  1. Humann 3.0 and bowtie metaphlan output
  2. Input Specification if Pre-Existing MetaPhlAn Files
  3. Question about using MetaPhlAn3 output as input for HUMAnN3

I had bowtie & sam files from metaphlan and the I used

humann -i $sample_sam -o $sample_out --threads 45 --taxonomic-profile $sample_metaphlan.txt --input-format sam

generated results with something like “UNMAPPED 0.0000000000 UNINTEGRATED 0.0000000000”

Now I have to run humann with raw input fasta file. So the bowtie & sam files from metaphlan have not useful for humann in any way?



If you’ve already run MetaPhlAn on your samples you can skip that step in HUMAnN by passing the existing taxonomic profile to HUMAnN via the --taxonomic-profile flag. You would pass your input reads and specify an output folder as normal.