Open SalvatoreRa opened 5 years ago
I think this is the same issue reported in https://support.bioconductor.org/p/120429/
Ensembl have closed my support ticket, so perhaps it is fixed?
I am not so sure, I found an alternative solution:
mart <- useEnsembl(biomart = "ensembl",
dataset = "hsapiens_gene_ensembl",
mirror = "useast") #changed mirror site, because otherwise it did not work
gene_list <- getBM(attributes=c('affy_hugene_1_0_st_v1', 'hgnc_symbol'),
filters = 'affy_hugene_1_0_st_v1',
values = gene_list,
mart = mart)
I'm having a similar problem with both the getSequence and getGene funcgtions of this package.
I'm having a similar problem with both the getSequence and getGene funcgtions of this package.
I do not know in your case, my solution for me is working (changing the mirror site)
I'm having a similar problem with both the getSequence and getGene funcgtions of this package.
I do not know in your case, my solution for me is working (changing the mirror site)
Is there a list of potential mirrors that I try changing to?
https://m.ensembl.org/info/about/mirrors.html
The valid options are ’www’, ’uswest’, ’useast’, ’asia’.
Hi I am having the same issue getting the sequence. Your help are highly appreciated @grimbough . Thanks a lot!
mart <- useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl",
# version="112",
# host = "https://asia.ensembl.org",
# host = "https://www.ensembl.org",
mirror = "asia",
verbose=TRUE)
mart information:
Formal class 'Mart' [package "biomaRt"] with 8 slots
..@ biomart : chr "ENSEMBL_MART_ENSEMBL"
..@ host : chr "https://www.ensembl.org:443/biomart/martservice?redirect=no"
..@ vschema : chr "default"
..@ version : chr ""
..@ dataset : chr "hsapiens_gene_ensembl"
..@ filters :'data.frame': 435 obs. of 9 variables:
Querying successful without flanking option:
biomaRt::getSequence(id=c("ENSG00000205571"), type="ensembl_gene_id",
seqType="gene_exon",
mart=mart) %>% tibble
Output:
# A tibble: 36 × 2
gene_exon ensembl_gene_id
<chr> <chr>
1 TCTGTGAAGTAGCTAATAATATAGAACAAAATGCTCAAGAG ENSG00000205571
2 ATAATTCCCCCACCACCTCCCATATGTCCAGATTCTCTTGATGATGCTGATGCTTTGGGAAGTATGTTAATTTCATGGTACATGAGTGGCTATCATACTGGCTATTATATGGTAAGTAATCACTCAGCA… ENSG00000205571
3 AGTCTCGCTCTGCTGCCCACGCTGGAGTGCAGTGGTGCAATCTCAGCTCACTGCAACCTCTGCTATCCGGGTTCAAGCAGTTCTCGTGCCTCACCCACGTGAGTAGTTGGGATTACAGGCATGTGGCAC… ENSG00000205571
4 CATGCTCTAAAGAATGGTGACATTTGTGAAACTTCGGGTAAACCAAAAACCACACCTAAAAGAAAACCTGCTAAGAAGAATAAAAGCCAAAAGAAGAATACTGCAGCTTCCTTACAACAG ENSG00000205571
5 ATGGCGATGAGCAGCGGCGGCAGTGGTGGCGGCGTCCCGGAGCAGGAGGATTCCGTGCTGTTCCGGCGCGGCACAGGCCAG ENSG00000205571
6 GAAATGCTGGCATAGAGCAGCACTAAATGACACCACTAAAGAAACGATCAGACAGATCTGGAATGTGAAGCGTTATAGAAGATAACTGGCCTCATTTCTTCAAAATATCAAGTGTTGGGAAAGAAAAAA… ENSG00000205571
7 AGCCAGGTCTAAAATTCAATGGCCCACCACCGCCACCGCCACCACCACCACCCCACTTACTATCATGCTGGCTGCCTCCATTTCCTTCTGGACCACCA ENSG00000205571
8 ATAATTCCCCCACCACCTCCCATATGTCCAGATTCTCTTGATGATGCTGATGCTTTGGGAAGTATGTTAATTTCATGGTACATGAGTGGCTATCATACTGGCTATTATATGGTAA ENSG00000205571
9 CCAGGTCTAAAATTCAATGGCCCACCACCGCCACCGCCACCACCACCACCCCACTTACTATCATGCTGGCTGCCTCCATTTCCTTCTGGACCACCA ENSG00000205571
10 GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTAAATTAAGGA ENSG00000205571
# ℹ 26 more rows
# ℹ Use `print(n = ...)` to see more rows
Failed query with flanking option:
biomaRt::getSequence(id=c("ENSG00000205571"), type="ensembl_gene_id",
seqType="gene_exon",
downstream=5,
mart=mart) %>% tibble
Error:
Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery, :
Query ERROR: caught BioMart::Exception::Usage: Filter downstream_flank NOT FOUND
sessionInfo:
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
[10] biomaRt_2.61.0 purrr_1.0.2 furrr_0.3.1 future_1.33.2 UpSetR_1.4.0 here_1.0.1
loaded via a namespace (and not attached):
[1] KEGGREST_1.42.0 gtable_0.3.5 httr2_1.0.1 Biobase_2.62.0 tzdb_0.4.0 vctrs_0.6.5
[7] tools_4.3.1 bitops_1.0-7 generics_0.1.3 parallel_4.3.1 stats4_4.3.1 curl_5.2.1
[13] fansi_1.0.6 AnnotationDbi_1.64.1 RSQLite_2.3.7 blob_1.2.4 pkgconfig_2.0.3 dbplyr_2.5.0
[19] S4Vectors_0.40.2 lifecycle_1.0.4 GenomeInfoDbData_1.2.11 compiler_4.3.1 Biostrings_2.70.3 progress_1.2.3
[25] munsell_0.5.1 codetools_0.2-19 GenomeInfoDb_1.38.8 RCurl_1.98-1.14 pillar_1.9.0 crayon_1.5.2
[31] cachem_1.1.0 parallelly_1.37.1 tidyselect_1.2.1 digest_0.6.35 stringi_1.8.4 listenv_0.9.1
[37] rprojroot_2.0.4 fastmap_1.2.0 grid_4.3.1 colorspace_2.1-0 cli_3.6.2 magrittr_2.0.3
[43] utf8_1.2.4 withr_3.0.0 prettyunits_1.2.0 filelock_1.0.3 scales_1.3.0 rappdirs_0.3.3
[49] bit64_4.0.5 timechange_0.3.0 XVector_0.42.0 httr_1.4.7 globals_0.16.3 bit_4.0.5
[55] gridExtra_2.3 png_0.1-8 hms_1.1.3 memoise_2.0.1 IRanges_2.36.0 BiocFileCache_2.10.2
[61] rlang_1.1.4 Rcpp_1.0.12 glue_1.7.0 DBI_1.2.3 xml2_1.3.6 BiocGenerics_0.48.1
[67] rstudioapi_0.16.0 R6_2.5.1 plyr_1.8.9 zlibbioc_1.48.2
Hi,
I am using getSequence to retrieve upstream sequence of a gene. I followed the example that I found in the vignette but it did not work.
I tried the following code and that the first time worked:
the problem is that is not working anymore. If I clean the global environment and test again sometimes works sometimes not. Most of the time I just get the following error: