PhyloPhlAn version 3.0.67 (24 August 2022)
I am using 222 genomes to create a phylogenetic tree using Phylophlan3. I wanted to get marker DNA for each genome (to use it for other analysis) but I am only getting 202 makers files, meaning for 20 genomes, it’s missing. On checking, even the final tree also has only those 202 genomes. I then checked the intermediate files, only clean_dna and map_dna has files for all 222 genomes, from next steps, only 202 genomes are considered. Also, since all my genomes come from the same genus, I expected them to have similar (number of) markers. Please help me with this. In the meantime, I will rerun Phylophlan3 on the same inputs.