Francesco Asnicar

Dear Davi, Many thanks for the outputs. I do believe this is fixed in the latest version that is only in Github and not in Bioconda yet. Can I ask...

Yes, agree, only thing is before pushing a new version to Bioconda I'm waiting to collect enough commits/edits (which probably is the case now). So, if Davi is able to...

Thanks Davi. So, my interpretation here is the following: * the config file `supertree_nt.cfg` is not present in the local folder; * PhyloPhlAn tried to find it in the standard...

Thanks Davi! Which dependencies were missing? (They shouldn't as they are specified in the package, but I'm curious to understand what could be the problem here) About the `[e] both...

Thanks! So, that's really strange that you were missing those tools, but that explains the error, the config file for some reason was wrongly created without the twos sections because...

Hi Valter, Many thanks for reporting this. As currently there is a slightly newer version in the repository, will you be able to pull PhyloPhlAn from the repo and run...

Hi Valter, yes, that's correct (sorry it might be confusing a bit). `3.0.2` is the version of the PhyloPhlAn package in Bioconda, which is not the same as the version...

Thank you both for reporting this issue. From a quick look it seems that this is due to old IDs in the PhyloPhlAn coreness files that are not resolved by...

Hi all, with commit c64a75fc3841507ce4a6264616f81140bce01009 this issue should be fixed. Can I ask you to pull the latest version from the repository and test it? I'll then make a new...

Ah right! Sorry, I forgot to mention that the new APIs from UniProt need the `requests` package to be installed. You can add it to your `phylophlan-dev` by running: ```...