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?
Sorry, I should have shown the output .txt file:
#mpa_v30_CHOCOPhlAn_201901
#/home/brucesteel/miniconda2/envs/mpa/bin/metaphlan MB2_trimmomatic_R1_paired.fastq.gz,MB2_trimmomatic_R1_unpaired.fastq.gz,MB2_trimmomatic_R2_paired.fastq.gz,MB2_trimmomatic_R2_unpaired.fastq.gz --bowtie2out MB2.bowtie2.bz2 --input_type fastq
#SampleID Metaphlan_Analysis
#clade_name NCBI_tax_id relative_abundance additional_species
k__Bacteria 2 100.0
k__Bacteria|p__Firmicutes 2|1239 86.57248
k__Bacteria|p__Proteobacteria 2|1224 13.42752
k__Bacteria|p__Firmicutes|c__Bacilli 2|1239|91061 86.57248
k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria 2|1224|28221 13.42752
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales 2|1239|91061|186826 86.57248
k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales 2|1224|28221|213118 13.42752
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae 2|1239|91061|186826|1300 86.57248
k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae 2|1224|28221|213118|213119 13.42752
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus 2|1239|91061|186826|1300|1357 86.57248
k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfobacter 2|1224|28221|213118|213119|2289 13.42752
k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus|s__Lactococcus_chungangensis 2|1239|91061|186826|1300|1357|451457 86.57248
k__Bacteria|p__Proteobacteria|c__Deltaproteobacteria|o__Desulfobacterales|f__Desulfobacteraceae|g__Desulfobacter|s__Desulfobacter_hydrogenophilus 2|1224|28221|213118|213119|2289|2291 13.42752
It is possible that the third species is present in the metagenome in low abundance and/or there are not present markers for identify the species. You could try lowering the stat_q value for letting MetaPhlAn considering more markers