I am trying to build an up to date EnsDB following the vignette. I have the ensembl PERL API installed. fetchTablesFromEnsembl() is running, but extremely slowly. After about 2 hours, I have 3 meg of text files.
> fetchTablesFromEnsembl(90, species = "mouse")
Connecting to ensembldb.ensembl.org at port 5306
# get_gene_transcript_exon_tables.pl version 0.3.0:
Retrieve gene models for Ensembl version 90, species mouse from Ensembl database at host: ensembldb.ensembl.org
Start fetching data
$ du -shc *.txt
PID USERNAME THR PRI NICE SIZE RES STATE C TIME WCPU COMMAND
76085 esiefker 1 20 0 139M 76464K sbwait 0 1:28 0.91% perl
Perl is spending all its time in 'sbwait'. (FreeBSD 11) Any ideas on how to improve this?
Would be included but the forum is telling me:
"Language "af" is not one of the supported languages ['en']!"