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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
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re-use database folder #60

Open pxtm opened 3 years ago

pxtm commented 3 years ago

Hi,

I've been using Phylophlan for a while now in few MAG-related projects. Is there a chance of, when I am reusing the same database for annotating the genomes, to reuse the database already downloaded? I tried with --database-folder but I am still asked to download it again.

Thanks a lot. Bests, Marc

fasnicar commented 3 years ago

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 this is not working? I'll be happy to have a look.

Many thanks, Francesco

pxtm commented 3 years ago

Hi Francesco,

Yes, it's phylophlan_metagenomic. The version I am using is > PhyloPhlAn version 3.0.58 (8 September 2020) with the following code, as you indicate in the website tutorial phylophlan_metagenomic -i MAGs_vamb/bins/ -o phylo2 --nproc 4 -n 1 -d SGB.Jan19 --database_folder bins_SGB.Jan9 --verbose 2>&1 | tee phylo2.log If needed I can provide the log as far as I can edit out the paths. Thanks in advance.

fasnicar commented 3 years ago

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

pxtm commented 3 years ago

Hi @fasnicar, the content of the folder is the one you are indicating yeah.

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fasnicar commented 3 years ago

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 provide back the log for me to check?

Many thanks