Hi there,

I was trying to build the txdb file using the makeTxDbFromBiomart, however, I came across with an error.

The command I typed was :

dicty_txdb <-  makeTxDbFromBiomart(biomart="protists_mart",
                                      dataset="ddiscoideum_eg_gene",
                                      host="protists.ensembl.org")

The error message shows:

Download and preprocess the 'transcripts' data frame ... Error in 
getBM(attributes, filters = bm_filters, values = bm_values, ...) : 
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql 
database protists_mart_38: DBI connect('database=protists_mart_38;host=hh-
mysql-eg-mart-web.ebi.ac.uk;port=4599','ensro',...) failed: Can't connect to 
MySQL server on 'hh-mysql-eg-mart-web.ebi.ac.uk' (111) at /nfs/public/release/ensweb/live/eg_mart/www_91/protists/lib/BioMart/Configuration/DBLocation.pm line 98.

Could you give some suggestions?

Thanks!

Simon

Hi Simon,

I can reproduce this with the current release version of GenomicFeatures (1.36.2). I tried with various datasets (ddiscoideum_eg_gene, tgondii_eg_gene, pvivax_eg_gene) and all of them gave me the same error that you got. This is actually easy to reproduce with a simple biomaRt query:

library(biomaRt)
mart <- useMart("protists_mart", "tgondii_eg_gene", host="protists.ensembl.org")
attribs <- listAttributes(mart)
attribs[1:4, 1:2]
#                    name          description
# 1       ensembl_gene_id       Gene stable ID
# 2 ensembl_transcript_id Transcript stable ID
# 3    ensembl_peptide_id    Protein stable ID
# 4       ensembl_exon_id       Exon stable ID
bm_result <- getBM(c("ensembl_gene_id", "ensembl_transcript_id"), mart=mart)
# Error in getBM(c("ensembl_gene_id", "ensembl_transcript_id"), mart = mart) : 
#   Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database protists_mart_38: DBI connect('database=protists_mart_38;host=hh-mysql-eg-mart-web.ebi.ac.uk;port=4599','ensro',...) failed: Can't connect to MySQL server on 'hh-mysql-eg-mart-web.ebi.ac.uk' (111) at /nfs/public/release/ensweb/live/eg_mart/www_91/protists/lib/BioMart/Configuration/DBLocation.pm line 98.

This removes GenomicFeatures from the equation.

FWIW I know this was working until yesterday because the man page for makeTxDbFromBiomart() contains an example that tries to access tgondii_eg_gene, and, according to the last build report (from this morning), GenomicFeatures passed R CMD check:

  https://bioconductor.org/checkResults/3.6/bioc-LATEST/GenomicFeatures/malbec1-checksrc.html

I also get a lot of errors when querying the mart using their web interface:

  https://protists.ensembl.org/biomart/martview

For example, after selecting the "Toxoplasma gondii genes" dataset and the "Gene stable ID" and "Transcript stable ID" attributes, clicking on "Count" produces a "Dataset Caught Exception".

This removes biomaRt and RCurl from the equation.

Unfortunately, it seems that in the last few days the Ensembl marts got more flaky and unreliable than usual. This is why yesterday I turned off the makeTxDbFromBiomart() examples that try to access the metazoa and plants marts in GenomicFeatures (1.30.3):

  https://github.com/Bioconductor/GenomicFeatures/commit/ff1e33ec9618e12b2954dda12b6f59989378b410

  https://github.com/Bioconductor/GenomicFeatures/commit/6f28d14687f1d018dc1f0ce7284898eaf066dcb2

Now it's the turn of the protists mart to cause problems :-/

Can someone please contact the Ensembl folks to let them know? There is a link to their "Helpdesk" here:

  https://uswest.ensembl.org/info/about/contact/index.html

You could also wait and try again later.

The good news is that I have a patch for the devel version of GenomicFeatures that lets you use makeTxDbFromEnsembl() to query the protists mart and other Ensembl marts. I still need to test, document, and apply.

Cheers,
H.