Fetch transcripts and genes from Ensembl ... OK
Fetch exons and CDS from Ensembl ... OK
Fetch chromosome names and lengths from Ensembl ...Error in .fetch_Ensembl_chrominfo(dbconn, seq_region_ids = seq_region_ids, :
identical(colnames(seq_region), joined_columns) is not TRUE
For information, I got the same error using makeTxDbFromEnsembl but makeTxDbFromBiomart works properly (here I'm getting the release 89 / May 2017 for Mus musculus):
There appears to be an issue with an internal function that may need to be addressed. But you probably don't need to build your own TxDb; you can get comparable objects from AnnotationHub with much less fuss:
> library(AnnotationHub)
> hub <- AnnotationHub()
snapshotDate(): 2018-04-30
> query(hub, c("homo sapiens","EnsDb"))
AnnotationHub with 6 records
# snapshotDate(): 2018-04-30
# $dataprovider: Ensembl
# $species: Homo Sapiens
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH53211"]]'
title
AH53211 | Ensembl 87 EnsDb for Homo Sapiens
AH53715 | Ensembl 88 EnsDb for Homo Sapiens
AH56681 | Ensembl 89 EnsDb for Homo Sapiens
AH57757 | Ensembl 90 EnsDb for Homo Sapiens
AH60773 | Ensembl 91 EnsDb for Homo Sapiens
AH60977 | Ensembl 92 EnsDb for Homo Sapiens
> txdb <- hub[["AH60977"]]
require( ensembldb )
downloading 1 resources
retrieving 1 resource
|======================================================================| 100%
> txdb
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: 0.3.1
|Creation time: Sun Apr 8 01:11:55 2018
|ensembl_version: 92
|ensembl_host: localhost
|Organism: homo_sapiens
|taxonomy_id: 9606
|genome_build: GRCh38
|DBSCHEMAVERSION: 2.1
| No. of genes: 65256.
| No. of transcripts: 225358.
|Protein data available.
And while this object is an EnsDb rather than a TxDb, it is based on EBI/EMBL annotations, and is the current release, and is much faster and easier to get than building your own.
Thanks! That's very helpful! I wasn't aware that you could get the latest Ensembl annotations from AnnotationHub(). I knew about the EnsDb.Hsapiens.v86 package, but that's quite outdated by now.
For information, I got the same error using makeTxDbFromEnsembl but makeTxDbFromBiomart works properly (here I'm getting the release 89 / May 2017 for Mus musculus):
TxDb_EnsRel89_Mm <- makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl", host="may2017.archive.ensembl.org")