[biomart-users] errors with makeTxDbFromBiomart and gramene

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[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

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[biomart-users] Re: errors with makeTxDbFromBiomart and gramene

Mike Smith
Hi,

Sorry for the delay reply to this.  If you have questions about using Bioconductor packages, you are much more likely to get a quick response if you post on their support site at http://support.bioconductor.org

The error message you get with the gramene mart is a bit misleading.  It's nothing to do with your internet connection, but their mart is configured in a way that breaks biomaRt.  There is a configuration file that still points to a no longer existing server address, and biomaRt reads this file and then fails to find the old server.  This probably won't be fixed unless they change that file.

I would recommend you try connecting to the plants.ensembl.org mart which I think is more up-to-date anyway e.g.

library("biomaRt")
ensembl_plants <- useMart(biomart = "plants_mart", host="plants.ensembl.org")
listDatasets(ensembl_plants)

Regards,
Mike


On Monday, 13 March 2017 09:56:11 UTC+1, [hidden email] wrote:

Hi,


When running this command:

 

txdb <- makeTxDbFromBiomart (biomart="plants_mart", dataset="athaliana_eg_gene", host="<a href="http://plants.ensembl.org/" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fplants.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEQuhNay3XaHmYHQGWA3ybILgLhRg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fplants.ensembl.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEQuhNay3XaHmYHQGWA3ybILgLhRg&#39;;return true;">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 <a href="ftp://ftp.ensembl.org/pub/current_mysql/" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;ftp://ftp.ensembl.org/pub/current_mysql/&#39;;return true;" onclick="this.href=&#39;ftp://ftp.ensembl.org/pub/current_mysql/&#39;;return true;">ftp://ftp.ensembl.org/pub/current_mysql/

 

The other issue is when trying to use Gramene Biomart:

> library(biomaRt)

> listMarts(host="<a href="http://ensembl.gramene.org/" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fensembl.gramene.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHty2urNHwd3d0rlvKwHI56lfN31g&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fensembl.gramene.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHty2urNHwd3d0rlvKwHI56lfN31g&#39;;return true;">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="<a href="http://ensembl.gramene.org/" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fensembl.gramene.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHty2urNHwd3d0rlvKwHI56lfN31g&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fensembl.gramene.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHty2urNHwd3d0rlvKwHI56lfN31g&#39;;return true;">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 <a href="http://www.biomart.org/" style="color:rgb(17,85,204)" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.biomart.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFvFQb8gPW7ii4UdmnxgOd0Yc5jag&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.biomart.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFvFQb8gPW7ii4UdmnxgOd0Yc5jag&#39;;return true;">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

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