When using metaphlan3 and humann3, I found there was a discrepancy between metaphlan3 and Humann3 in profiling microbiota.
The versions of metaphlan3 and humann3 are “MetaPhlAn version 3.0 (20 Mar 2020)” and “humann v3.0.0.alpha.4” respectively.
My code for metaphlan3 is
nohup metaphlan sub_M1_35000000.fq --nproc 4 --input_type fastq --no_map -o profiled_metagenome_M1.txt > log_M1 2>&1 &
Code for humann3 is
nohup humann -i sub_M1_35000000.fq.gz -o ./ --threads 8 --output-basename M1 --diamond ~/toolkit/diamond --remove-temp-output > log_M1 2>&1 &
I noticed that the annotated species from humann3 are more than from metaphlan3. And I found that some differential genes or pathways were assigned to the species that were absent in the results of metaphlan3. So I have no idea what happened. How can I interpret the result of humann3? Or it there anything I misunderstood?
Thanks in advance!