Francesco Asnicar

Hi and thanks for reporting this. From these lines: ``` Inputs already cleaned Loading files from "input_genomes_phylophlan/tmp/clean_dna" "phylophlan" markers already mapped (key: "map_dna") ``` it seems it is not the...

Hi and thanks for reporting this. I think the problem here is that you might have created the config file using the `--force_nucleotides` param, but did not specify it when...

Hi and sorry for the late reply. So, I looked around, and potentially that could be due to the wrong handling of markdown files. So I just added a `.gitattributes`...

Hi, the `bin2meta.tsv` as described in the tutorial is a: > mapping file that links each bin to the metagenome it has been reconstructed from. It is a tab-separated file...

Hi Eric, thanks for the suggestion. I added a search for the executables and if not found reverting back to the script name. This should fix if you have PhyloPhlAn...

Dear Pablo, many thanks for using PhyloPhlAn. So, I believe you downloaded twice the same set of UniRef90s for the same taxonomic label, correct? If that's the case and you...

Dear @alexhbnr, thanks for following up on this. UniProt APIs recently changed and I've updated PhyloPhlAn as you can read here https://github.com/biobakery/phylophlan/issues/98. Did you try this latest version or are...

Hi, I believe we are talking about `phylophlan_metagenomic`, right? In which case, the `--database_folder` param should do exactly that. Can you provide the version you're using an example in which...

Thank for the command. So, is `bins_SGB.Jan9` a folder containing the files (` .md5`, `.txt.bz2`, `.tar`) of the `SGB.Jan19` db?

Hi, can you try to get the very latest version of `phylophlan_metagenomic.py` (should be `3.0.36 (3 February 2021)`) re-trying running it specifying the existing database with the `--database_folder` and then...