Entering edit mode
3.5 years ago
nitandressa
▴
10
Hello everyone!
so, I'm trying to retireve some information from biomaRt and just found this error:
> library(biomaRt)
> ensembl = useMart(host='http://sep2019.archive.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL', dataset='hsapiens_gene_ensembl')
> unique(ad.b.wb.a3.3$groupID)
[1] "ENSG00000168280" "ENSG00000144867" "ENSG00000091513" "ENSG00000242337"
[5] "ENSG00000197971" "ENSG00000279811" "ENSG00000106125" "ENSG00000241644"
[9] "ENSG00000240583" "ENSG00000250424" "ENSG00000254959" "ENSG00000273269"
[13] "ENSG00000143933" "ENSG00000239605" "ENSG00000173786" "ENSG00000007237"
> et = getBM(attributes=c("ensembl_gene_id","external_gene_name","gene_biotype"),
filters = "ensembl_gene_id",
values = unique(ad.b.wb.a3.3$groupID),
mart = ensembl)
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
cannot open compressed file '/tmp/biomaRt/5ea3405a17cc_file5ea353305cde', probable reason 'No such file or directory'
I don't know why this error is happening. The object exists and the vector had the ids. Most curious, if I remove one of the ids, it works:
> et = getBM(attributes=c("ensembl_gene_id","external_gene_name","gene_biotype"),
filters = "ensembl_gene_id",
values = unique(ad.b.wb.a3.3$groupID)[1:15],
mart = ensembl) # Minus the last element
> et = getBM(attributes=c("ensembl_gene_id","external_gene_name","gene_biotype"),
filters = "ensembl_gene_id",
values = unique(ad.b.wb.a3.3$groupID)[2:16],
mart = ensembl) # Minus the 1st element
> et = getBM(attributes=c("ensembl_gene_id","external_gene_name","gene_biotype"),
filters = "ensembl_gene_id",
values = unique(ad.b.wb.a3.3$groupID)[c(1:6,8:16)],
mart = ensembl) #Minus the 7th element
I also trying saving it in a different vetor, but the same error happened:
> aa=c("ENSG00000168280","ENSG00000144867","ENSG00000091513","ENSG00000242337","ENSG00000197971","ENSG00000279811","ENSG00000106125","ENSG00000241644","ENSG00000240583","ENSG00000250424","ENSG00000254959","ENSG00000273269","ENSG00000143933","ENSG00000239605","ENSG00000173786","ENSG00000007237")
> et = getBM(attributes=c("ensembl_gene_id","external_gene_name","gene_biotype"), filters = "ensembl_gene_id", values = aa, mart = ensembl)
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
cannot open compressed file '/tmp/biomaRt/5ea3405a17cc_file5ea353305cde', probable reason 'No such file or directory'
Here is the sessionInfo():
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Fedora 30 (Workstation Edition)
Matrix products: default
BLAS/LAPACK: /homes/brauerei/natasha/miniconda2/envs/r4/lib/libopenblasp-r0.3.10.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] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicAlignments_1.24.0 Rsamtools_2.4.0
[3] Biostrings_2.56.0 XVector_0.28.0
[5] SummarizedExperiment_1.18.2 DelayedArray_0.14.1
[7] matrixStats_0.57.0 GenomicFeatures_1.40.1
[9] AnnotationDbi_1.50.3 Biobase_2.48.0
[11] GenomicRanges_1.40.0 GenomeInfoDb_1.24.2
[13] IRanges_2.22.2 S4Vectors_0.26.1
[15] BiocGenerics_0.34.0 ComplexUpset_0.5.17
[17] ggplot2_3.3.2 pathview_1.28.1
[19] gageData_2.26.0 gage_2.38.3
[21] dplyr_1.0.2 biomaRt_2.44.1
[23] tidyr_1.1.2
loaded via a namespace (and not attached):
[1] httr_1.4.2 bit64_4.0.5 assertthat_0.2.1
[4] askpass_1.1 BiocManager_1.30.10 BiocFileCache_1.12.1
[7] blob_1.2.1 GenomeInfoDbData_1.2.3 progress_1.2.2
[10] pillar_1.4.6 RSQLite_2.2.1 lattice_0.20-41
[13] glue_1.4.2 digest_0.6.25 colorspace_1.4-1
[16] Matrix_1.2-18 XML_3.99-0.5 pkgconfig_2.0.3
[19] zlibbioc_1.34.0 purrr_0.3.4 GO.db_3.11.4
[22] patchwork_1.0.1 scales_1.1.1 BiocParallel_1.22.0
[25] tibble_3.0.3 openssl_1.4.3 KEGGREST_1.28.0
[28] generics_0.0.2 farver_2.0.3 ellipsis_0.3.1
[31] withr_2.3.0 cli_2.0.2 magrittr_1.5
[34] crayon_1.3.4 memoise_1.1.0 KEGGgraph_1.48.0
[37] fansi_0.4.1 graph_1.66.0 tools_4.0.2
[40] prettyunits_1.1.1 hms_0.5.3 org.Hs.eg.db_3.11.4
[43] lifecycle_0.2.0 stringr_1.4.0 munsell_0.5.0
[46] compiler_4.0.2 rlang_0.4.7 grid_4.0.2
[49] RCurl_1.98-1.2 rappdirs_0.3.1 bitops_1.0-6
[52] labeling_0.3 gtable_0.3.0 DBI_1.1.0
[55] curl_4.3 R6_2.4.1 rtracklayer_1.48.0
[58] bit_4.0.4 Rgraphviz_2.32.0 stringi_1.5.3
[61] Rcpp_1.0.5 vctrs_0.3.4 png_0.1-7
[64] dbplyr_1.4.4 tidyselect_1.1.0
Can anyone help me? Thanks in advance
Natasha
