Trouble running example 2 - Tree of Life

[sierra-smith]

Hello!

I am attempting to run example 2 in order to recreate the microbial tree of life and I am having trouble downloading the reference genomes.

First, I was having trouble downloading the assembly_summary_genbank.txt file remotely so I manually downloaded it and placed it in my environment.

Then, I tried to rerun phylophlan_get_reference \ -g all \ -o input_genomes/ \ -n 1 \ --verbose 2>&1 | tee logs/phylophlan_get_reference.log

And received the error message:

File "taxa2genomes.txt" present File "taxa2genomes_cpa201901_up201901.txt.bz2" present Output folder "input_genomes/" present File "assembly_summary_genbank.txt" present Downloading 1 reference genomes for kBacteria|pActinobacteria|cActinobacteria|oActinomycetales|fActinomycetaceae|gActinomyces|s__Actinomyces_radingae Downloading "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/106/055/GCA_900106055.1_IMG-taxon_2630968294_annotated_assembly/GCA_900106055.1_IMG-taxon_2630968294_annotated_assembly_genomic.fna.gz" to "input_genomes/GCA_900106055.fna.gz" [e] unable to download "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/106/055/GCA_900106055.1_IMG-taxon_2630968294_annotated_assembly/GCA_900106055.1_IMG-taxon_2630968294_annotated_assembly_genomic.fna.gz"

Can you please let me know what may be causing the problem? I am running this on MacOS Ventura 13.4.

Thank you! Sierra