Error with makeTxDbFromBiomart
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anavmar1 • 0
@8f378497
Last seen 15 months ago
Spain

Hello everyone! I'm trying to do an analysis with DEXSeq, but for that I need to connect to biomart first. I need to use the makeTxDbFromBiomart function to generate the TxDb object, but I always get the same error. I have already solved the firewall problem and if I should be able to connect to the internet, I don't know what is not working. Maybe someone can help me.

I attach the executed command and the error that it returns:

hse = makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl", host="https://www.ensembl.org")

Ensembl site unresponsive, trying useast mirror Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped) 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) : Failed to connect to ftp.ensembl.org port 21: Operation timed out

Thanks in advance! Alejandra

DEXSeq biomaRt • 1.2k views
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@james-w-macdonald-5106
Last seen 1 day ago
United States

Are you sure you need that TxDb? The easier thing to do would be to use an EnsDb that you can get from the AnnotationHub.

> library(AnnotationHub)

> hub <- AnnotationHub()
snapshotDate(): 2023-04-24
> query(hub, c("mus musculus","ensdb"))
AnnotationHub with 38 records
# snapshotDate(): 2023-04-24
# $dataprovider: Ensembl
# $species: Mus musculus, Mus musculus musculus, Mus musculus domesticus, Mu...
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH53222"]]' 

             title                                        
  AH53222  | Ensembl 87 EnsDb for Mus Musculus            
  AH53726  | Ensembl 88 EnsDb for Mus Musculus            
  AH56691  | Ensembl 89 EnsDb for Mus Musculus            
  AH57770  | Ensembl 90 EnsDb for Mus Musculus            
  AH60788  | Ensembl 91 EnsDb for Mus Musculus            
  ...        ...                                          
  AH109651 | Ensembl 109 EnsDb for Mus musculus           
  AH109652 | Ensembl 109 EnsDb for Mus musculus           
  AH109653 | Ensembl 109 EnsDb for Mus musculus musculus  
  AH109654 | Ensembl 109 EnsDb for Mus musculus domesticus
  AH109655 | Ensembl 109 EnsDb for Mus musculus           
> ensdb <- hub[["AH109655"]]
loading from cache
require("ensembldb")
> ensdb
EnsDb for Ensembl:
|Backend: SQLite
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.3.10
|Creation time: Fri Feb 17 05:48:03 2023
|ensembl_version: 109
|ensembl_host: localhost
|Organism: Mus musculus
|taxonomy_id: 10090
|genome_build: GRCm39
|DBSCHEMAVERSION: 2.2
|common_name: mouse
|species: mus_musculus
| No. of genes: 57010.
| No. of transcripts: 149443.
|Protein data available.
>

You might need to try several versions to ensure you are matching up to whatever version was used to align your data.

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Thanks James, I will try this.

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@herve-pages-1542
Last seen 18 hours ago
Seattle, WA, United States

The Ensembl Mart is notoriously unreliable, but it looks like it's working today:

txdb <- makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl") 
# 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 ... OK
# Make the TxDb object ... OK

txdb
# TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Mus musculus
# Taxonomy ID: 10090
# Resource URL: www.ensembl.org:443
# BioMart database: ENSEMBL_MART_ENSEMBL
# BioMart database version: Ensembl Genes 110
# BioMart dataset: mmusculus_gene_ensembl
# BioMart dataset description: Mouse genes (GRCm39)
# BioMart dataset version: GRCm39
# Full dataset: yes
# miRBase build ID: NA
# Nb of transcripts: 149547
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2023-08-11 18:57:14 -0700 (Fri, 11 Aug 2023)
# GenomicFeatures version at creation time: 1.52.1
# RSQLite version at creation time: 2.3.1
# DBSCHEMAVERSION: 1.2

Note that an alternative to makeTxDbFromBiomart() is to use makeTxDbFromEnsembl(). The latter will query the Ensembl MySQL server _directly_ (and thus bypass the Mart service completely):

txdb2 <- makeTxDbFromEnsembl("Mus musculus")
# Fetch transcripts and genes from Ensembl ... OK
#   (fetched 149547 transcripts from 56941 genes)
# Fetch exons and CDS from Ensembl ... OK
# Fetch chromosome names and lengths from Ensembl ...OK
# Gather the metadata ... OK
# Make the TxDb object ... OK

txdb2
# TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: Ensembl
# Organism: Mus musculus
# Ensembl release: 110
# Ensembl database: mus_musculus_core_110_39
# MySQL server: ensembldb.ensembl.org
# Full dataset: yes
# Nb of transcripts: 149547
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2023-08-11 18:50:42 -0700 (Fri, 11 Aug 2023)
# GenomicFeatures version at creation time: 1.52.1
# RSQLite version at creation time: 2.3.1
# DBSCHEMAVERSION: 1.2

See ?makeTxDbFromEnsembl for more information, including how to specify a given Ensembl release.

Best,

H.

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