If an input genome is named as an accession number (eg. GCF_000111222.gbff) and this genome is also identified and downloaded, then somehow this taxon gets renamed in the concatenated alignment file. This causes the name of the input genome to match the name for the genome that was automatically downloaded by phantasm. Subsequently, the duplicate taxon in the alignment file will cause FastTree and/or IQTree to fail.
If an input genome is named as an accession number (eg. GCF_000111222.gbff) and this genome is also identified and downloaded, then somehow this taxon gets renamed in the concatenated alignment file. This causes the name of the input genome to match the name for the genome that was automatically downloaded by phantasm. Subsequently, the duplicate taxon in the alignment file will cause FastTree and/or IQTree to fail.