makeTxDbFromBiomart cannot open URL
Hello, I am trying to make a Txdb-like object from Ensembl annotation of drerio_gene_ensembl but it throws that Error:
Error in download.file(url, destfile, method, quiet = TRUE) :
cannot open URL 'ftp://ftp.ensembl.org/pub/release-115/mysql/'
My code is:
txdb_ensembl <- makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL",
host="https://www.ensembl.org", dataset="drerio_gene_ensembl")
Has anyone encountered this problem yet?
Thank you very much!
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https://ftp.ensembl.org/pub/release-115/mysql/will work. Most websites have switched to usinghttpsoverftpfor these kinds of data.Are you using the latest version of BioMart?
Hey now it throws the error: Error in 'req_perform()' HTTP 404 Not Found
I tried using: host="https://ftp.ensembl.org/pub/release-115/mysql/" and then host="https://ftp.ensembl.org"
Something is off because this directory exists and contains the wanted annotation.
Also, I am using biomaRt 2.62.1
Thanks!
Are you using GenomicFeatures package (rather than BiomaRt directly)?
Current BiomaRt appears to be v.2.66 so you are a few versions off. Can you update to the latest and see if that helps.
Not sure if you need to create an issue on BiomaRt GitHub site: https://github.com/Huber-group-EMBL/biomaRt/issues or GenomicFeatures site: https://github.com/Bioconductor/GenomicFeatures/issues