Hello,

I run this command to make a txDb object from biomart. 

txdb <- makeTxDbFromBiomart(biomart="fungal_mart",dataset="bgraminis_eg_gene",transcript_ids=NULL,host="fungi.ensembl.org")

I get this:

Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... Error in function (type, msg, asError = TRUE)  : 
  Server denied you to change to the given directory

As the problem seems very similat tp this query Getting errors with makeTxDbFromBiomart I downloaded the B.graminis gtf file from ftp://ftp.ensemblgenomes.org/pub/fungi/release-36/gtf/blumeria_graminis/ but also get an error:

dbFile <- ensDbFromGtf("Blumeria_graminis.EF1.36.gtf.gz")

Importing GTF file ... OK
Error in dimnames(x) <- dn : 
  length of 'dimnames' [2] not equal to array extent
In addition: Warning message:
In .Method(..., deparse.level = deparse.level) :
  number of columns of result is not a multiple of vector length (arg 2)

Could someone please help me with this ?

Many thanks

Indeed, there was a bug in ensDbFromGtf that failed to parse the GTF header properly (the genome version contained a white space). I've fixed that and will push the fix to Bioconductor soon.

In the meanwhile you can download the EnsDb package for your species using the link below

https://www.dropbox.com/s/zx5os4e1zt0w6rp/EnsDb.Bgraminis.v89_2.1.tar.gz?dl=0

cheers, jo