The bioBakery help forum

Which folder should I put phy_database in?

Hi,
I’ve been working on your tutorial recently

https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-3.0

StrainPhlAn: metagenomic strain-level population genomics

when I run step5, it says StrainPhlAn will call PhyloPhlAn to produce a multiple sequence alignment (MSA) to then build the phylogenetic tree. then I get an error

strainphlan -s consensus_markers/*.pkl -m db_markers/s__Bacteroides_caccae.fna -r reference_genomes/G000273725.fna.bz2 -o output -n 8 -c s__Bacteroides_caccae --phylophlan_mode accurate --mutation_rates 

Tue May 12 12:37:58 2020: Start StrainPhlAn 3.0 execution
Tue May 12 12:37:58 2020: Creating temporary directory...
Tue May 12 12:37:58 2020: Done.
Tue May 12 12:37:58 2020: Getting markers from main sample files...
Tue May 12 12:38:00 2020: Done.
Tue May 12 12:38:00 2020: Getting markers from main reference files...Warning: [blastn] Examining 5 or more matches is recommended

Tue May 12 12:38:17 2020: Done.
Tue May 12 12:38:17 2020: Removing bad markers / samples...
Tue May 12 12:38:17 2020: Done.
Tue May 12 12:38:17 2020: Writing samples as markers' FASTA files...
Tue May 12 12:38:18 2020: Done.
Tue May 12 12:38:18 2020: Writing filtered clade markers as FASTA file...
Tue May 12 12:38:18 2020: Done.
Tue May 12 12:38:18 2020: Calculating polymorphic rates...
Tue May 12 12:38:19 2020: Done.
Tue May 12 12:38:19 2020: Executing PhyloPhlAn 3.0...
Tue May 12 12:38:19 2020: 	Creating PhyloPhlAn 3.0 database...
Tue May 12 12:38:23 2020: 	Done.
Tue May 12 12:38:23 2020: 	Generating PhyloPhlAn 3.0 configuration file...
Tue May 12 12:38:24 2020: 	Done.
Tue May 12 12:38:24 2020: 	Processing samples...[e] unable to download "https://www.dropbox.com/s/x7cvma5bjzlllbt/phylophlan_databases.txt?dl=1"

[e] An error was ocurred executing a external tool, exiting...
Tue May 12 12:38:56 2020: Stop StrainPhlAn 3.0 execution.

I can’t download databases from wget, then I download this database from chrome. So my question is

Which folder should I put this database in?

my metaphlan3 version is
MetaPhlAn version 3.0 (20 Mar 2020)

Hi, thanks for reporting this.

I think this should be under the StrainPhlAn category and most likely the best person to ask bout this is @aitor.blancomiguez who is developing StrainPhlAn.

Many thanks,
Francesco