Error in bmRequest(request = request, httr_config = httr_config, verbose = verbose) : Gateway Timeout (HTTP 504).
1
0
Entering edit mode
21 months ago
JACKY ▴ 150

I am using this code to extract the lengths of genes directly from ensemble:

  ensembl = useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl")
  genelength =  getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id', 'transcript_length','cds_length'), filters =  'ensembl_gene_id', values = rownames(counts), mart = ensembl, useCache = FALSE)
  gene_canonical_transcript =  getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id','transcript_is_canonical'), filters =  'ensembl_gene_id', values = rownames(counts), mart = ensembl, useCache = FALSE)
  gene_canonical_transcript_subset = gene_canonical_transcript[!is.na(gene_canonical_transcript$transcript_is_canonical),]
  genelength = merge(gene_canonical_transcript_subset, genelength, by = c("ensembl_gene_id", "ensembl_transcript_id"))
  return(genelength)

This however doesn't always work, I really don't know why it works only 50% of the time. Sometimes it uses mirror sites:

Ensembl site unresponsive, trying uswest mirror

sometimes it works perfectly fine without using mirror sites, and sometimes it fails completely, producing this error:

Error in bmRequest(request = request, httr_config = httr_config, verbose = verbose) :
Gateway Timeout (HTTP 504).

What causes this to be so unstable? I mean, the code works just fine (it gives gene lengths when it runs without any errors). Is the problem with the package? or with the site itself? is there anyway to avoid this error?

Thank you.

r ensemble biomart • 3.2k views
ADD COMMENT
0
Entering edit mode

Out of interest, why are you setting cache = FALSE? The caching is designed for cases where you've already run a query and then want to run exactly the same thing again on a different day. It should load the results from disk and be much faster (especially if the Ensembl server isn't working). If the version of Ensembl changes or you ask for slightly different information then the cache will be ignored automatically, even if it's set to cache = TRUE. My hope is that the cache can really help out in some situations without ever getting in the way, so I'm curious why you want to turn it off.

ADD REPLY
1
Entering edit mode
21 months ago
Mensur Dlakic ★ 27k

It is the same reason we sometimes stream movies without problems, and other times there is lots of buffering. Network traffic varies, plus they have to do site maintenance from time to time. There is nothing to be done to fix it - try at a different time.

ADD COMMENT

Login before adding your answer.

Traffic: 2727 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6