The bioBakery help forum

Is there some database update than "taxa2core_cpa201901_up201901.txt.bz2"?

Dear asnicar

There is smoe genes that I can’t download, is the uniref website change gene name?

phylophlan_setup_database \
    -g s__Bacteroides_vulgatus \
    -o ./s_vulgatus/ \
    --verbose 2>&1 | tee log/phylophlan_setup_database.log
[e] unable to download "http://www.uniprot.org/uniref/UniRef90_A0A396ANJ6.fasta"
Downloading "http://www.uniprot.org/uniref/UniRef90_A0A0N7J7J7.fasta" to "./s_vulgatus/s__Bacteroides_vulgatus/A0A0N7J7J7.faa"
[e] unable to download "http://www.uniprot.org/uniref/UniRef90_A0A0N7J7J7.fasta"
Downloading "http://www.uniprot.org/uniref/UniRef90_R7KG75.fasta" to "./s_vulgatus/s__Bacteroides_vulgatus/R7KG75.faa"
[e] unable to download "http://www.uniprot.org/uniref/UniRef90_R7KG75.fasta"
Downloading "http://www.uniprot.org/uniref/UniRef90_A0A0K2HE35.fasta" to "./s_vulgatus/s__Bacteroides_vulgatus/A0A0K2HE35.faa"
[e] unable to download "http://www.uniprot.org/uniref/UniRef90_A0A0K2HE35.fasta"
Downloading "http://www.uniprot.org/uniref/UniRef90_A0A076IMH5.fasta" to "./s_vulgatus/s__Bacteroides_vulgatus/A0A076IMH5.faa"

Is there some database update than “taxa2core_cpa201901_up201901.txt.bz2” ?

Dear @CK_zhu,

The errors you see are “normal” as UniRef proteins change their IDs over time. However, phylophlan_setup_database will keep track of them and try to resolve the new names for those proteins in a second step. If there are still proteins that could not be downloaded, those will be reported in a file named: s__Bacteroides_vulgatus_core_proteins_not_mapped.txt (you’ll find it inside the s_vulgatus folder you specified in the command line). You can check how many proteins were not downloaded reported in the above file if present.

We don’t have an updated version yet, but there will be an update soon.

Thanks,
Francesco