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Question: errors with makeTxDbFromBiomart
0
gravatar for Marie
3 months ago by
Marie0
Marie0 wrote:

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

 

 

 

ADD COMMENTlink modified 3 months ago by Johannes Rainer1.1k • written 3 months ago by Marie0

I'll have a look into this. If everything else fails I'll create the EnsDb using the Ensembl perl API.

 

cheers, jo

ADD REPLYlink written 3 months ago by Johannes Rainer1.1k
0
gravatar for Johannes Rainer
3 months ago by
Johannes Rainer1.1k
Italy
Johannes Rainer1.1k wrote:

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

ADD COMMENTlink written 3 months ago by Johannes Rainer1.1k

I've now pushed the fix (for Bioconductor release 3.5 and Bioconductor 3.6 development version) to Bioc svn. Means within the next few days an updated version of ensembldb (version 2.0.4) should be available that can generate the EnsDb also from the GTF. To update ensembldb:

library(BiocInstaller)
biocLite("ensembldb")

 

cheers, jo

ADD REPLYlink written 3 months ago by Johannes Rainer1.1k
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