Hi All,

I've been running into a problem with biomaRt and while I've seen a few other posts describe a similar problem, none of them are quite the same as mine  so I'm asking for your wisdom.

I've been trying to collect upstream sequences using "coding_gene_flank" from the current human ensembl assembly and whether I provide just one ENSG name or a vector of 1000s, whether I ask for 100 or 2000 upstream or downstream bps, regardless of my request, I get a query error saying that there there is no upstream_flank filter/downstream_flank filter found. I do not encounter this problem when getting sequences from the genomes of other species.  I'm not running loops or doing anything particularly fancy. I'm not sure what's going on. 

Here is my code using a few ENSG ids (as an example) and the error - I'm running R version 3.2.3 , biomaRt 2.24.1

ensembl <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="www.ensembl.org")

Human2 = c("ENSG00000000419", "ENSG00000000457", "ENSG00000000938")

Human1200 = getSequence(id = Human2, type="ensembl_gene_id",seqType="coding_gene_flank",upstream=1200, mart=ensembl)

Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"),  :
  Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT FOUND

And here it is for mouse, which is working fine

ensemblm <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl", host="www.ensembl.org")

Mouse2 = c("ENSMUSG00000078919", "ENSMUSG00000093752", "ENSMUSG00000026584")

MMus2 = getSequence(id= Mouse2, type="ensembl_gene_id", seqType="coding_gene_flank", upstream=1200, mart=ensemblm)

Thanks for your help.

Daub.

You are running an old version of (at least) biomaRt on a current install of R (the version of biomaRt you are using is intended for R-2.1). Try upgrading and see if it helps.

> ensembl <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="www.ensembl.org")
> Human2 = c("ENSG00000000419", "ENSG00000000457", "ENSG00000000938")
> Human1200 = getSequence(id = Human2, type="ensembl_gene_id",seqType="coding_gene_flank",upstream=1200, mart=ensembl)
> Human1200                                                              coding_gene_flank
1 TTACCTGTTGTCACCCTGTGAGTTTGTATCCCTGTTGTCAAGAAAGCTGTTCATATTGTAGAAGATTTGGAAGGTGCAGGCAAGTGTGTGTGTATAAAATTACCTATAATCTGACCTTCCACTGGAAACCTCTGTTAATACTTCAACATATATTTTTCAAGTCTGTGTGTATGTATACATATATTTCTTTTCAAAACAACTTTGAGGCGTAATTGATACAGAATAAATGAAAAAAGTGTACAGTTTTATGTTTTGACATAATCACCCGTTACCATCATCATCATCAAGATAATGAATATATCCATCCTCCCAAAAGTTCCTCATACATCATGATAATCCTTTCCTCTCCCTTGATCCCTCTAACTGTGCCCCTTCACTAGGTGAGCACTGAAGTATTTTGTCATAGTTGCATTTGAATTCTGTGTATGTGTGGGCTTTTGTTTTTTTTTAGCAATTGAGATTATTTGAGATTCAGTTTTGCGGTTTCCCCTTTTTACTTAGGATAGCTTTGAAGAGTAGTGCGATCGTACTTTTTCTTATGTTTATCGTCATTTGTGTTTCTTCAATGAGTTGTCTGTTTTCTTTCCCATTATTGTACTGGTGTTTTAGTGTTTTACTTGGTTTATATGAGCTCTTCATTTGTTAATATGTTTTTCATCATATTAACAATGTTTTTCAACATATTAATATTAAAACCATGATTTTCCTCATTATAAGTATTCTCCAATTTGTATTGTTTTCCTTTATAATTTTAAGTTATTTTCTACATACAGAAGTTTTATTGTTTTTGAGTAATATTTTTACAACATTTTCCTTTGTGAGTGAGGATATACAAGTGAGTTAGGAAGTATGAATTACCTTATTCTATTTTTGATTGCCTTTCCACTCTGAAAGTTTGTATGTGGTGGAGTTTGGGGAGGGACAGTAACTACCTGTGACTATTTAGTAATGTGCATTTTCTCTAGAGCTGTTAGTTGTTAATTAACAACCATTGCTGGTAACTTGCAGAGCGTTTACCATTTTTACTGTCAAATGTCCTAGTTATGAGGATCAAAGAAACTAGTAGTTTGGGGTGGCTATGTCTGGATATCTCTTGTTGATGTTGCAGATAGGGATTTAATGTTTGAAATTGTTTTCTGTTTTCTTTTAGATCTGCTTGGCTTTGAGGAAGAGTGGCAGTACTGCCTCACTGCATAAGGG
2 CTGCGGCTCCGCAGCCGAATAGAGCGGAAATGCCCTCTCAGGGCATCAAAGAGCAACAAGCTGCCACTGTAAGAGGGGCCCAGACCCGCAGCGATTTTCAGCACTTCCAAGGCCTGCAGGCAGCCCAGGACCCCGGTAACGACACCGAGCACCCCGCCGTCCGCGCAGTTGGTCACTGTCTCCGCTGGGGGTGGTTGGGGGAATATGCAGCGATAGCAAGGGCCACCGTCATAATGGTAGACTGTGATTTGGCCCTCGAAGCGCAAGGCACTGGCAGACACGAGGGGCCGACCCGCCAGCACACATGCGTCATTAACCAGGTAGCGAGTGGGCACGTTGTCCGAGCAGTCAGCCACCACATCATATCGGCGGACCAGGTCTAGGGCAGTGGCTGGCGTAAGGGCCTGAGTGTACGGCACGCATTCCACTGCCGAATTGAGGCGGCGCAGCGAGGCGGCGGCCGAAAAGGCCTTGGCCTGGCCAGCCAGTGCCTCGCCATGCAGCACTTGGCGGGCCAGGTTGCTCATCTCTACCACGTCATAGTCCACAAGGCCAAGGCGGCCCACGCCGGCCGCTGCCAAGTACTGCGCTAGTGGACAGCCGAGCCCACCGCAGCCCACGATTAGCACGCACGCGGTCCCCAGGCGCAGCTGTCCGTGCACGCCCAGCTCGGGCAGCACTAGCTGCCGGCTATAGCGCAGAATCTCATCTCGGGACAGAGCGGCCTTCGGCGGCAGCGGCGACACCGGAACCAGCCGTTCTGGCTGCGGTTCCTGCTCAGCCAAAAGAGCCGACGCCAGCTTCTGCTTCAGCGAATTCAATTCCTCCTCACGTTGGGCAACTTCAGCTTGTAAGGCGAGTACCTCCTCCCGGGAAGCCATGGCGACCTCTTCCGGAAGTTGTCGTGAAAGGCATTTCCGCTTCCGTCTTCTGTCTCCTAGCGACTGGGATAAACTAAAAAACTTTATGGAGCTTGGGAAAAGGTGATGAATAGATATTTACTTCCTGAAGAAACCTTCAGATTAAACTTCAAAGATGTATAAATCCAGAATATTTCTAATTGAACCACGCAATGGCCCTAGAAGAACTAGCGATCAATCACACAGGTCATCCCCCGCTTCCGAATTTGGTACGGTCCGACCCGTCCTTTTCCGCGCCACATTACGTAATTCCGCTTCCGGCATCTGGCTCAGTTCCGCC
3 CACTGACCCAGGAGTAGGGGCCTAAGGGGTGAGTGGGGTAGACTGAGGGCTTTCAGGGTCAGGAAACAGGGTGGGGGTGGCCTTCCTGAACCCCACAACTCCTCACAGCCTCCTCCTCCTACAAGGACCCTGTTGCTAGGTAACGGATGGGGGAGCCAGAATGAGGCAGCTTGAGAGGCTGAAGGCTGGACCCACGACAGGAAATGGCCTTGATCCCCCTCTGCAGTGACTCTCCAGGTGCAGACACACAGCCTCACACACACTCACACACAAACATGCGCAGATATATAGACATACATGCAGAGATACACACATCCAGAGACAGGCACACTGCTCCCACACAGAGATAGGTGCACATTCATAGACACACAGACACAGAGACACCCACTCACACAGACAGGCACACACATACTCACACAGAAACACATGCACACAAACACGGTCTTACAGACATATACACATGCAGCCAAACACATACACAGAGACTTTTATACACTCTCGTATACACACAAACCTGCACACACAGACAGACATCCACAAAGAGCTGCACACACATGCATACCCACACAGGCAAACTCACCCATACTTAGAGACACACAAAGACGCACATGTACAAGCACACTGAAAGAGTCACAGAAACACAACATATCAAAGCAATAGGACCCAACCTGAGCAATATAGCAAGACCTTGTCTCTACTAAAAATCAAACAAATTAGCCAGGGGTACTGGCACGCACCTGTATAGTCCCAGTTCTTGGGAGGCTGAGACCAGAGGATCACTTGAGCCCAGGAGATCAAGGCTGCAGCAAGCTATGATTGTGCCACTGCACTCCAGCCTGGGCAACAGAGTGAGATCTTGTCTCAAAACAAAACAAAAAAAGCAAAGCAATAGGAGGCAAAAATATGCAAATAAGCATAGCAATATCCCAATGTAGAAAGCCAGCCCCAGAGATATAGACATGAGCCAATGGGAAGAGAAGCACTGAGGGGGGACATACTGTGAGGCAGACTGAACGGTACAGTAGGTGGCCCAGTTCCGCCTTTATCCCTTACAGGGAGGACCCCAATCTAGGCCCAAGAGGGAAAGCCACGTGCCTGTATGAGCGTATGAGCATGTGCATGCGCGTGTGTGCACAGGGTGGTGCACCTGGCAGGGGTCCTTGAGTGAGGCATGCCCCATTCTGTAGCAGGGAACCTGGA
  ensembl_gene_id
1 ENSG00000000457
2 ENSG00000000419
3 ENSG00000000938
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] biomaRt_2.26.1

Hi James, 

Thanks! So I updated the biomaRt package and I have the same problem, just different error language. Now I get this when I run the code for human  

Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

When I run the code for mouse, everything is still fine. I get the sequences. My connectivity is fine. I'm kind of stumped.