I just downloaded the new version of metaphlan 3.1 and I have a problem when I add the --add_viruses option I don’t have any virus in output.
When I did it with metaphlan 3.0 it worked. Do you have any idea?
Thank you so much for your help
I’m here to better explain my issue. When I ran Metaphlan with this command line :
metaphlan I1_R1_R2.bowtie2.bz2 --bowtie2out I1_R1_R2.bowtie2.bz2 --nproc 8 --input_type bowtie2out -o profiled_metagenome_I1_R1_R2_VIRUSES.txt --ignore_bacteria --add_viruses
I obtain a table with some virus (100%), if I remove --ignore_bacteria option I had a table with 100% bacteria and no virus. If I add --unknown_estimation I obtain a table with 54% bacteria, 47% unknown and no virus…
I don’t understand at all what happens…