biomaRt getBM() returns nothing most of the times
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@laurenzholcik-20105
Last seen 19 months ago

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

biomaRt getBM • 340 views
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swbarnes2 ▴ 890
@swbarnes2-14086
Last seen 3 hours ago
San Diego

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.

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I did yes. It's just that it says that some services are not available and I understand that it would be slower, but no returning anything without any error seems more like a bug to me? And also I was using the US hosts, so I thought maybe if just the European servers are migrating that would help..

Anyways right now it's working fine again but I guess that later in the day (European time) it will start making problems.

If anyone can confirm that they have the same problems or that they know that it's because of the server migration that would also be helpful then I know I just have to wait a few days :)

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The Ensembl team contacted me about this a few months ago, and my understanding was that the main BioMart service should be fine. The regional mirrors should be completely unaffected, and backup hardware will be serving the main site while they migrate to the new data centre. I guess there's potential for the main site to still be slow, but it the US mirror should be fine.

To try and answer the question about whether anyone else is having the same problem, are you the researcher from University of Bath who emailed me yesterday? If not, then there's at least one person experiencing very similar issues!

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No I did not contact you. Okay thanks, then I know it's not a problem on my side at least.

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I have had problems access ensembl the other day, the US mirrors; when the exact same command line sometimes works, sometimes does not.

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