Quantcast

[biomart-users] errors with makeTxDbFromBiomart and gramene

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

[biomart-users] errors with makeTxDbFromBiomart and gramene

hediatnani0

Hi,


When running this command:

 

txdb <- makeTxDbFromBiomart (biomart="plants_mart", dataset="athaliana_eg_gene", host="plants.ensembl.org")

 

I get this:

 

Download and preprocess the 'transcripts' data frame ... OK

Download and preprocess the 'chrominfo' 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 .Ensembl_getMySQLCoreDir(dataset) : 

  found 0 or more than 1 subdir for "athaliana_eg_gene" dataset at ftp://ftp.ensembl.org/pub/current_mysql/

 

The other issue is when trying to use Gramene Biomart:

> library(biomaRt)

> listMarts(host="ensembl.gramene.org")

                 biomart                 version

1     ENSEMBL_MART_PLANT          Plant Genes 52

2 ENSEMBL_MART_PLANT_SNP Plant Variation Mart 52

> gramene= useMart(biomart = "ENSEMBL_MART_PLANT", host="ensembl.gramene.org")

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.

Error in if (BioMartVersion == "\n" | BioMartVersion == "") { : 

  argument is of length zero


Please can you help me with these issues.

Regards,
H

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.
Loading...