I would like to generate a phylogentic tree of 120 de-replicated MAGs of which 84 are bacteria and 36 are archaeal MAGs.
However when we run all the 120 MAGs together I get only 101 MAGs on the RAxML_bestTree.Genome_peat_refined.tre. Kindly advice why 19 MAGs are not reflected in the tree.
In addition we also separately performed a phylogenetic tree of 36 archaeal MAGs we got only 19 MAGs in the tree. Why is this the case?
Ideally I would like to have all the MAGs that I have inputed to come out on the tree.
Script used:
phylophlan -i $INPUT_DIR/ -o $OUTPUT_DIR -d phylophlan --databases_folder /export2/home/phylophlan_databases --diversity low -f /export2/home/miniconda3/lib/python3.7/site-packages/phylophlan/phylophlan_configs/supermatrix_aa.cfg --nproc 28 -t a --force_nucleotides --genome_extension “.fasta”