Francesco Asnicar

Glad it worked! The error with astral is known and not an error per see, actually. When you run a gene tree pipeline, ASTRAL cannot be automatically installed, so you...

Hi, the problem is that you used the `supermatrix_nt.cfg` which contains standard settings for a nucleotide database (`_nt`, and also from the `[dn_dna]` section you posted you can see that...

Hi, the old version 2.0 that was available in Bitbucket was basically an improvement over PhyloPhlAn v1.0, but at a certain point, that version couldn't be improved further. So, when...

Hi, reading through the error you reported it feels to me that there is a problem with the Biopython library. Please, check if there exists a Biopython version compatible with...

Dear @GriffyGe, thanks for reporting this. I think your problem is due to a wrong configuration figuessI gues the error is because `blastn` can't find a properly indexed database. With...

Hi, first of all, thanks for using PhyloPhlAn! So, I think the problem is with the `--proteome_extension "faa.gz"`, you don't actually need to provide the compressed extension there. What should...

Hi there, not specifically as an option. You could though either _(1)_ kill the job as soon as the MSA step is done, _(2)_ edit the code to introduce a...

Dear Gaofeng, PhyloPhlAn is compatible with earlier versions of Diamond, the problem is that earlier versions were faster because of a bug, so your results might be biased as not...

Hello, from the log it seems you only provided 3 input files, while the minimum number for building a phylogenetic tree is 4. Hence all markers are discarded because only...

Hi, thank you for using PhyloPhlAn and reporting this. Have you tried running the command from the error output file? `/home/kyle/miniconda3/envs/phylophlan/bin/diamond blastx --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps...