Francesco Asnicar

Hi Eric, got it! The links you provided are for the `phylophlan_metagenomic` and are not the `phylophlan` and `amphora2` databases. I think the easiest thing to do is to create...

Great! Yes, I'll add this to the wiki. About the env variable, I'll implement it in the following release, although I believe that for non-computational people the param is easier...

Hi Eric, I see and you're right if the file system is read-only then one has to perform also the decompression and indexing. I'll add this, thank you. Although an...

Hi Pedro, Thank you for reporting this. The command line you specified define a "gene tree" pipeline and not a concatenation one, like in old PhyloPhlAn versions. If you want...

Hi Pedro, Great! To count the actual number of markers, it depends on the pipeline and the cleaning steps performed on the MSAs. What you should count is not the...

Hi, the `-n` parameter is an "up to" for each single species. To make an example, let's assume you specify (as you reported above): ~~~ phylophlan_get_reference -g g__Acinetobacter -o input_genomes/...

Hello Pablo, Apologies, but I'm not sure to which log you're referring. You already put the `--verbose` and saved the output from PhyloPhlAn to the log file `logs/phylophlan__output-228-apr2022.log`. Within the...

Hi Pablo, To answer your questions: > i) The number of files in the "markers" folder represents the total number of markers detected? Yes, that would be the number of...

Hi, it seems maybe you're not running the very last version you pulled from the repo, is that the case? My best guess would be that your `phylophlan` command is...

Hi, do you also have a local `phylophlan_substitution_matrices` where you executed PhyloPhlAn? If so, that will override the package folder `miniconda3/env/phylophan/lib/python3.10/site-packages/phylophan/phylophan_subsitution_matrices`. Alternatively, you can use the `--submat_folder` param to specify...