Hey everyone,

I am trying to obtain exon sequences and ensembltranscriptid_versions from the database. Depending on the time of day, most of the times I execute getBM() I get nothing back, also no error. It lookds like this:

> test = getBM(attributes = c('gene_exon','ensembl_transcript_id_version'),
+              filters = c('ensembl_gene_id'),
+              values = 'ENSMUSG00000022884', mart = mouse, verbose = TRUE)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= 'biomaRt'> <Dataset name = 'mmusculus_gene_ensembl'><Attribute name = 'gene_exon'/><Attribute name = 'ensembl_transcript_id_version'/><Filter name = "ensembl_gene_id" value = "ENSMUSG00000022884" /></Dataset></Query>
#################
Results from server:
[1] "Exon sequences\tTranscript stable ID version\n"
#################
Parsed results:
[1] Exon sequences               Transcript stable ID version
<0 rows> (or 0-length row.names)

If I execute the same line again sometimes I get a result, sometimes not. I am using this in a larger script to automate a workflow it would therefore be important that this is reliable. In the code above it works sometimes at the moment, but I use getBM in a loop over several marts because I need sequences of several organisms. Strangely, in the loop it works even fewer times. Currently I'm on host 'useast.ensembl.org', I've tried 'www.ensembl.org' which is slower but otherwise same result.

Thanks!

Laurenz

Did you see this?

http://www.ensembl.info/2020/02/18/reduced-functionality-16th-25th-march-2020/

Things might just be flaky for the next week or so. That might be some of the problem.