Hi,
I found that reads matching to eukaryotic (e.g. fungal species such as Aspergillus) are not reported in the profile output.
It states that k_bacteria has a relative abundance of 100% but only 130,000 reads.
The reason can be discovered in the bowtie files, 98% of the reads are mapped to 293939__A0A0S7DXK2 (Aspergillus lentulus.)
How would you check for contamination with eukaryotic reads ? Is it recommended to use tools like kraken before running metaphlan ? Can metaphlan report eukaryotic matches ?
Best, Michael