Metaphlan and Humann data analysis

Hi all
I am sorry, because I am reposting this query again, because I thought I have posted in wrong place.
Please ignore mistakes.
After performing the taxonomic and functional analysis of Shotgun dataset in Metaphaln and humanN, I have got my data in terms of relative abundance. I have also got biom files for each data sample:
Can we convert the biom files into OTU table and then use in R for different downstream analysis.
If so, please help me with:

  1. Do i need to combine the biom files first
  2. I need the code to convert the biom to OTUs. Tsv file
    Thanks ans Regards

Hi again
Thanks, I converted the biom to Tsv using biom convert command.
However, I have still one issue that is:
As Metaphlan doesn't generate OTUs rather it gives relative abundance. But how can I get the OTUs for diversity analysis.
Any way to get it done
Thanks and Regards

Hi all
I searched through the forum and found a plugin
Error in Import · Issue #13 · gregcaporaso/q2-sapienns · GitHub
I successfully installed the plugin and tried withy my dataset, but got the error
I then tried to run the command qiime tools import --input-path Galaxy.tsv --output-path Galaxy_outPut.qza --type MetaphlanAbundanceTable and got the error
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/builtin/", line 157, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/", line 250, in import_data
output_dir_fmt = pm.get_directory_format(type_)
File "/home/qiime2/miniconda/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/", line 354, in get_directory_format
raise TypeError(
TypeError: Semantic type MetaphlanAbundanceTable does not have a compatible directory format.

An unexpected error has occurred:

Semantic type MetaphlanAbundanceTable does not have a compatible directory format.

See above for debug info.
I am also attaching the file , the analysis was carried out in Galaxy using Metaphlan

I found that the functionality was developed for the MetaPhlAn format that contains exactly two columns (clade_name and NCBI_tax_id ) before the sample abundance columns, but should also work if the NCBI_tax_id is not present (as is the case in MetaPhlAn 4 output). I recommend looking at the column headers for the first three columns in your input file before attempting to use this code:
But then I have one query here, how can we use this at different taxonomic levels (like phylum, class....)
kindly guide
thanks and Regards