Francesco Asnicar

Thank you for testing it out, I'm closing this then!

Dear Stephen, thanks for reporting this. We had issues with our FTP server. You can remove the `phylophlan_metagenomic.txt` file so that the updated one with the fixed URLs will be...

Hi, I think you need to either install or clone the GraPhlAn repository https://github.com/biobakery/graphlan. Many thanks, Francesco

Hi, I think it might be due to some connection instability. I re-run the command you posted this morning and it is still running (downloading genomes from NCBI). Are you...

Yes, you can play a bit with bash and the files downloaded by PhyloPhlAn at the beginning: `taxa2genomes_cpa0.2_up201804.txt.bz2` and `assembly_summary_genbank.txt`. 1. For each line in `taxa2genomes_cpa0.2_up201804.txt.bz2` you should consider the...

Hi, thanks for reporting this and for using PhyloPhlAn. From the log you posted, it is clear that this is not the first time you run PhyloPhlAn on these inputs....

Ok, thanks, then something is not right with the MSA probably. Have you tried run the FastTree command in the error: ``` /home/mwa/miniconda3/bin/FastTreeMP -pseudo -spr 4 -mlacc 2 -slownni -fastest...

Ok, can you check then that the MSA is a valid one? If not, probably something went wrong the first time you ran PhyloPhlAn and then I would suggest you...

Hi, how many inputs do you have in your input folders `/home/mwa/input_phylophlan`?

Ok, so that's the problem. You can't build a phylogeny with only one single genome/proteome.