database "phylophlan" not found in "phylophlan_databases"

[mcahn]

I've installed phylophlan (the version in today's github repo (2020-04-21), and I'm attempting to run Example-02:-Tree-of-life.

I've run phylophlan_get_reference, and created the config file:

phylophlan_write_config_file -d a \ -o 02_tol.cfg \ --db_aa diamond \ --map_dna diamond \ --map_aa diamond \ --msa mafft \ --trim trimal \ --tree1 iqtree \ --verbose 2>&1 | tee phylophlan_write_config_file.log

When I run phylophlan:

phylophlan -i input_genomes \ -d phylophlan \ -f 02_tol.cfg \ --diversity high \ --fast \ -o output_tol \ --nproc 8 \ --verbose 2>&1 | tee logs/phylophlan.log

I get this error:

[e] database "phylophlan" not found in "phylophlan_databases" Available databases in "phylophlan_databases":

Am I supposed to put something in phylophlan_databases before I run this example? Bear with me, I'm a sysadmin rather than a biologist.

Thanks, Matthew Cahn

[fasnicar]

Dear Matthew,

Thanks for reporting this. Since you specified -d phylophlan you should not put anything inside the phylophlan_databases folder, as it should be automatically downloaded. I think I did a fix yesterday that broke this part. It should now be fixed b4ccc17f5f8af864bcacfd72dea72b8cd1c73822. Can you update the code and try again?

Many thanks, Francesco

[mcahn]

Hi Francesco,

I think this is fixed. I did a "git pull", moved the phylophlan_databases directory out of the way, and ran the job again. This time phylophlan created the directory, but failed to do the download -- almost certainly because the compute nodes on our cluster can't reach out to the Internet. So in this environment the download would have to be done manually the way I did it before. Just for the record the error message was:

Downloading "https://www.dropbox.com/s/x7cvma5bjzlllbt/phylophlan_databases.txt?dl=1" to "phylophlan_databases/phylophlan_databases.txt" [e] unable to download "https://www.dropbox.com/s/x7cvma5bjzlllbt/phylophlan_databases.txt?dl=1"

Thanks very much for your help, Matthew

[fasnicar]

Hi Matthew,

Yes, the error is due to the fact that the node doesn't have internet access. I'm glad it works now.

Many thanks, Francesco