grimbough / biomaRt

R package providing query functionality to BioMart instances like Ensembl
https://bioconductor.org/packages/biomaRt/
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Error in curl::curl_fetch_memory(url, handle = handle) : #57

Open zillurbmb51 opened 2 years ago

zillurbmb51 commented 2 years ago

Hi, I was trying to map some chromosome:BP position to rsID and getting the above error. I have only 60 query. biomart version 2.51.3

> snp_mart <- useEnsembl(biomart="ENSEMBL_MART_SNP", 
+                        host="grch37.ensembl.org", 
+                        dataset="hsapiens_snp")
Warning message:
Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://" 
> rs1=getBM(attributes = c('refsnp_id', 'allele','chr_name', 'chrom_start'), 
+       filters = 'chromosomal_region', 
+       values = position1, 
+       mart = snp_mart)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [grch37.ensembl.org:80] Operation timed out after 300000 milliseconds with 0 bytes received

What I am doing wrong? How could I effectively convert chr:pos to rsID? Any Help?