Phylophlan Tree of life

Microbial community profiling PhyloPhlAn
1

Hi @f.asnicar
I was trying to download the reference genomes, and while trying to do that it stopped downloading several times so every time I deleted the assembly_summary_genbank.txt file and ran the command again which finally downloaded 17,287 reference genomes in total in the directory. I want to know how I get to know if all the reference genomes have been downloaded. Command that I gave:
phylophlan_get_reference -g all -o /lustre/TOL/REF_GENOMES/ -n 1

Thanks in Advance!

2

Hi @saras22,
I don’t have a straightforward way to do this check. But what I would try is to retrieve the taxonomic labels from the assembly_summary_genbank.txt file of the genomes downloaded into /lustre/TOL/REF_GENOMES/ and then check that there are no duplicated taxonomic labels.

Hope this helps,
Francesco