I have an issue using the functionality of the R package customProDB to download annotation data from Ensembl as described in the documentation (2.2 ENSEMBL annotation from BIOMART). To check for yourself use browseVignettes("customProDB"). I saw multiple other users had the issue in the past like here: GenomicFeatures makeTranscriptDbFromBiomart 'chrominfo' data frame ... FAILED! . However, those threads weren't useful to resolve my issue.

The issue is that it fails to download the 'chrominfo' data frame. A subsequent function of customProDB however needs that data.

How do I get the chrominfo?

# install necessary packages
# if (!requireNamespace("BiocManager", quietly = TRUE))
#   install.packages("BiocManager")
# 
# BiocManager::install("customProDB")

library(customProDB)
library(seqinr)
library(glue)
library(rtracklayer)

# open documentation in browser
# browseVignettes("customProDB")

# specify annotation data from ENSEMBL
ensembl <- useMart(
  "ENSEMBL_MART_ENSEMBL", 
  dataset="hsapiens_gene_ensembl",
  host="dec2021.archive.ensembl.org",
  path="/biomart/martservice", 
  archive=FALSE
)

# where to save the downloaded data
annotation_path <- "~/Documents/ncHLAII_immunopeptidomics/ensembl"
dir.create(annotation_path)

# download and save the annotation data
PrepareAnnotationEnsembl(
  mart=ensembl, 
  annotation_path=annotation_path, 
  splice_matrix=FALSE, 
  dbsnp=NULL, 
  COSMIC=FALSE
)

Output from Console:

Prepare gene/transcript/protein id mapping information (ids.RData) ...  done
Build TranscriptDB object (txdb.sqlite) ... 
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 ... OK
Make the TxDb object ...