Metaphlan Hidden contamination

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

Hi @MichaWeb75
Are all the 98% of the reads mapping against the same marker or to different markers of A. lentulus?

all the reads map to the same Aspergillus lentulus marker gene. I found that all of these reads are probably of mice origin, but apparently this Aspergillus marker gene the closest sequence in the database. This is important to notice that not all species are represented by the database.