Greetings to your nice forum.
I have finished running my analysis of metaphlan 3.0 on my datasets and trying to run all the marker analyses on the bowtie output. i used the code below
metaphlan -t marker_ab_table --bowtie2out metagenome_dataset1_.bowtie2.bz2 --nreads 9533350 --nproc 12 --input_type bowtie2out -o marker_abundance_table_dataset1.txt
but I don’t get any results… (the metagenomic profile has given a lot of taxonomies so I know I have a lot o f things as i have seen the txt output of metaphlan)