I have installed metaphlan3 according to the instructions on the website (https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-3.0) using Miniconda2 in the bioconda channel, and have created a separate environment for metaphlan3. I am using MetaPhlAn on trimmed paired and unpaired reads created by trimmomatic and Metaphlan seems to run with no problems with the following command:
metaphlan MG2_trimmomatic_R1_paired.fastq.gz,MG2_trimmomatic_R1_unpaired.fastq.gz,MG2_trimmomatic_R2_paired.fastq.gz,MG2_trimmomatic_R2_unpaired.fastq.gz --bowtie2out MG2.bowtie2.bz2 --input_type fastq > MG2_profiled_metagenome.txt
However, when I view the MG2_profiled_metagenome.txt file generated by MetaPhlAn, only two species of microorganism have been identified. Furthermore, when I assemble these reads using Megahit and look at the MetaQUAST assembly report, it appears that there are more than 2 species of microorganism within the metagenome, therefore suggesting that the MetaPhlAn profiled metagenome file is incorrect.
I was wondering if there are any problems that can cause this in MetaPhlAn3?