Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... Error in FUN(X[[i]], ...) :
1 unknown species: ‘Human genes’ Please use 'available.species' to see viable species names or tax Ids
Session info:
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.2 (Sierra)
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.24.0 dplyr_0.5.0 biomaRt_2.30.0 GenomicFeatures_1.26.2 AnnotationDbi_1.36.2
[6] Biobase_2.34.0 GenomicRanges_1.26.2 GenomeInfoDb_1.10.3 IRanges_2.8.1 S4Vectors_0.12.1
[11] BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.9 magrittr_1.5 XVector_0.14.0 zlibbioc_1.20.0 GenomicAlignments_1.10.0
[6] BiocParallel_1.8.1 R6_2.2.0 tools_3.3.1 SummarizedExperiment_1.4.0 DBI_0.5-1
[11] lazyeval_0.2.0 assertthat_0.1 tibble_1.2 rtracklayer_1.34.1 bitops_1.0-6
[16] RCurl_1.95-4.8 RSQLite_1.1-2 Biostrings_2.42.1 Rsamtools_1.26.1 XML_3.98-1.5
Maybe the problem is that you're not using the latest released version of Bioconductor (which is 3.4). Some fixes were applied recently to makeTxDbFromBiomart() in BioC 3.4 (and in BioC devel) to work around some issues introduced by some changes on the Ensembl Mart side.
Try to load the BiocInstaller package. You should see something like this:
> library(BiocInstaller)
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
A newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
I strongly suggest that you upgrade your installation to use BioC 3.4 so you get these fixes.
This error seems to be cropping up in GenomicFeatures:::.prepareBiomartMetadata, which is an internal function that isn't really intended for people to call directly. Regardless, we can call this function directly to see if we can get the error you see:
> mart <- useMart("ENSEMBL_MART_ENSEMBL", "cfamiliaris_gene_ensembl")
> GenomicFeatures:::.prepareBiomartMetadata(mart, TRUE, "ensembl.org", "80", "9615", "5")
Prepare the 'metadata' data frame ... OK
name value
1 Data source BioMart
2 Organism Canis familiaris
3 Taxonomy ID 9615
4 Resource URL www.ensembl.org:80
5 BioMart database ENSEMBL_MART_ENSEMBL
6 BioMart database version Ensembl Genes 87
7 BioMart dataset cfamiliaris_gene_ensembl
8 BioMart dataset description cfamiliaris_gene_ensembl
9 BioMart dataset version CanFam3.1
10 Full dataset yes
11 miRBase build ID 5
And as before, I can't reproduce the error. What happens if you try to do this?
Yes, you are right. Seems to be working now.
Thanks!
I'm getting the same error?
Weirdly, it works if I use an archived 'host'="jul2016.archive.ensembl.org"
Hi,
Maybe the problem is that you're not using the latest released version of Bioconductor (which is 3.4). Some fixes were applied recently to
makeTxDbFromBiomart()in BioC 3.4 (and in BioC devel) to work around some issues introduced by some changes on the Ensembl Mart side.Try to load the BiocInstaller package. You should see something like this:
I strongly suggest that you upgrade your installation to use BioC 3.4 so you get these fixes.
Cheers,
H.
This solved the problem, thank you
This error seems to be cropping up in GenomicFeatures:::.prepareBiomartMetadata, which is an internal function that isn't really intended for people to call directly. Regardless, we can call this function directly to see if we can get the error you see:
> mart <- useMart("ENSEMBL_MART_ENSEMBL", "cfamiliaris_gene_ensembl") > GenomicFeatures:::.prepareBiomartMetadata(mart, TRUE, "ensembl.org", "80", "9615", "5") Prepare the 'metadata' data frame ... OK name value 1 Data source BioMart 2 Organism Canis familiaris 3 Taxonomy ID 9615 4 Resource URL www.ensembl.org:80 5 BioMart database ENSEMBL_MART_ENSEMBL 6 BioMart database version Ensembl Genes 87 7 BioMart dataset cfamiliaris_gene_ensembl 8 BioMart dataset description cfamiliaris_gene_ensembl 9 BioMart dataset version CanFam3.1 10 Full dataset yes 11 miRBase build ID 5And as before, I can't reproduce the error. What happens if you try to do this?