Question: Anyone else having trouble with biomaRt (Oct 10, 2019)
0
gravatar for swbarnes2
9 weeks ago by
swbarnes2340
swbarnes2340 wrote:

I'm using a command line that should work fine, that worked fine all yesterday, and today it intermittently works.

> ensembl = useEnsembl(biomart='ensembl', dataset="rnorvegicus_gene_ensembl", mirror = 'uswest') 
> sequences <- getBM(attributes=c('ensembl_transcript_id', 'external_gene_name', 'ensembl_gene_id', 'ensembl_exon_id', 'rank', 'gene_exon'), filters = 'ensembl_transcript_id', values = new_transcripts, mart = ensembl)
> dim(sequences)
[1] 5699    6
> sequences <- getBM(attributes=c('ensembl_transcript_id', 'external_gene_name', 'ensembl_gene_id', 'ensembl_exon_id', 'rank', 'gene_exon'), filters = 'ensembl_transcript_id', values = new_transcripts, mart = ensembl)
> dim(sequences)
[1] 0 6

Those two getBM calls happened on after the other, with no changes at all in between. (Edit: Also, that 5699 result is only about half the results I should be getting) Is anyone else experiencing this?

Another test, these two command lines entered right after each other

> dim(test_sequences <- getBM(attributes=c('ensembl_transcript_id', 'external_gene_name', 'ensembl_gene_id', 'ensembl_exon_id', 'rank', 'gene_exon'), filters = 'ensembl_transcript_id', values = "ENSRNOT00000011731", mart = ensembl))
[1] 1 6
> dim(test_sequences <- getBM(attributes=c('ensembl_transcript_id', 'external_gene_name', 'ensembl_gene_id', 'ensembl_exon_id', 'rank', 'gene_exon'), filters = 'ensembl_transcript_id', values = "ENSRNOT00000011731", mart = ensembl))
[1] 0 6

SessionInfo

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /.automount/apps/illumina_tools/conda_test_env/lib/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.38.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1           AnnotationDbi_1.44.0 magrittr_1.5
 [4] BiocGenerics_0.28.0  hms_0.4.2            progress_1.2.0
 [7] IRanges_2.16.0       bit_1.1-14           R6_2.4.0
[10] rlang_0.4.0          httr_1.4.0           stringr_1.4.0
[13] blob_1.1.1           tools_3.5.1          parallel_3.5.1
[16] Biobase_2.42.0       DBI_1.0.0            bit64_0.9-7
[19] digest_0.6.18        assertthat_0.2.1     crayon_1.3.4
[22] S4Vectors_0.20.1     bitops_1.0-6         curl_3.3
[25] RCurl_1.95-4.12      memoise_1.1.0        RSQLite_2.1.1
[28] stringi_1.4.3        compiler_3.5.1       prettyunits_1.0.2
[31] stats4_3.5.1         XML_3.98-1.19        pkgconfig_2.0.2
biomart ensembl • 106 views
ADD COMMENTlink modified 9 weeks ago by Mike Smith4.0k • written 9 weeks ago by swbarnes2340

Can you update to include sessionInfo() so we can see the biomaRt version you're using. Normally when biomaRt fails to talk to Ensembl correctly you get an error rather than an empty result, so this may be something I haven't seen before.

Also, might be worth seeing if the same happens when using a different mirror.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Mike Smith4.0k

I added the mirror because it was what another older post recommended trying. Before that, I had no mirror, but version = 97

ADD REPLYlink written 9 weeks ago by swbarnes2340

I can confirm I'm seeing the same behaviour across several mirrors. This is going to be fun to diagnose!

ADD REPLYlink written 9 weeks ago by Mike Smith4.0k

So is it just the rat database that's not working right?

ADD REPLYlink written 9 weeks ago by swbarnes2340

I just tested rat with the same useEnsembl() code you provided, but different mirror arguments. I think it can't be universal because there are normally a ton of questions in short order if Ensembl / biomRt stops working entirely. I'll look more closely tomorrow.

ADD REPLYlink written 9 weeks ago by Mike Smith4.0k
Answer: Anyone else having trouble with biomaRt (Oct 10, 2019)
0
gravatar for Mike Smith
9 weeks ago by
Mike Smith4.0k
EMBL Heidelberg / de.NBI
Mike Smith4.0k wrote:

I can reproduce this problem in the Ensembl BioMart web interface. Just select the rat gene dataset and as for any sequence type & it will intermittently return zero results.

This indicates it's a problem at Ensembl's end, so I suggest raising a support ticket with them.

ADD COMMENTlink written 9 weeks ago by Mike Smith4.0k
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