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Question: Error in makeTxDbFromBiomart
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gravatar for katie_emelianova
4 weeks ago by
katie_emelianova0 wrote:

I'm getting an error in makeTxDbFromBiomart.
> makeTxDbFromBiomart()

The full stacktrace is:

Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... FAILED! (=>skipped)
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... Error in .prepareBiomartMetadata
    (mart, is_full_dataset, host, port, taxonomyId,  :
          the BioMart database "ENSEMBL_MART_ENSEMBL" has no (or more than
    one)
          "hsapiens_gene_ensembl" datasets
        In addition: Warning messages:
        1: In scan(con, sep = "\t", blank.lines.skip = TRUE, what =
    "character",  :
          EOF within quoted string
        2: In scan(con, sep = "\t", blank.lines.skip = TRUE, what =
    "character",  :
          EOF within quoted string


I had used it in the last week or so, so I don't believe it is a
firewall/security issue on my end. Also, I tried the same command but for
the C. elegans dataset and that worked fine.

I have also contacted Ensembl and I have tried running the following:

library(biomaRt)
ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
listDatasets(ensembl)


Which works, suggesting the problem is not on Ensembl's end.

Do you know whether the problem is on your end?

Best,

Katie

 

 

 

 

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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] AnnotationHub_2.12.1        biomaRt_2.36.1              GenomicAlignments_1.16.0    Rsamtools_1.32.3            Biostrings_2.48.0          
 [6] XVector_0.20.0              SummarizedExperiment_1.10.1 DelayedArray_0.6.6          BiocParallel_1.14.2         matrixStats_0.54.0         
[11] GenomicFeatures_1.32.3      AnnotationDbi_1.42.1        Biobase_2.40.0              GenomicRanges_1.32.7        GenomeInfoDb_1.16.0        
[16] IRanges_2.14.12             S4Vectors_0.18.3            BiocGenerics_0.26.0        

loaded via a namespace (and not attached):
 [1] progress_1.2.0                lattice_0.20-35               htmltools_0.3.6               rtracklayer_1.40.6            yaml_2.2.0                   
 [6] base64enc_0.1-3               interactiveDisplayBase_1.18.0 blob_1.1.1                    XML_3.98-1.16                 rlang_0.2.2                  
[11] later_0.7.5                   DBI_1.0.0                     bit64_0.9-7                   GenomeInfoDbData_1.1.0        stringr_1.3.1                
[16] zlibbioc_1.26.0               memoise_1.1.0                 evaluate_0.12                 knitr_1.20                    BiocInstaller_1.30.0         
[21] httpuv_1.4.5                  curl_3.2                      Rcpp_0.12.19                  xtable_1.8-3                  promises_1.0.1               
[26] backports_1.1.2               jsonlite_1.5                  mime_0.6                      bit_1.1-14                    hms_0.4.2                    
[31] digest_0.6.18                 stringi_1.2.4                 shiny_1.1.0                   grid_3.5.1                    rprojroot_1.3-2              
[36] tools_3.5.1                   bitops_1.0-6                  magrittr_1.5                  RCurl_1.95-4.11               RSQLite_2.1.1                
[41] crayon_1.3.4                  pkgconfig_2.0.2               Matrix_1.2-14                 prettyunits_1.0.2             assertthat_0.2.0             
[46] rmarkdown_1.10                httr_1.3.1                    rstudioapi_0.8                R6_2.3.0                      compiler_3.5.1 

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by katie_emelianova0

Is it doing this consistently?  It ran successfully for me just now - including the 'chrominfo' step that failed for you:

> makeTxDbFromBiomart()
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 ... OK
Make the TxDb object ... OK
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Homo sapiens
# Taxonomy ID: 9606
# Resource URL: www.ensembl.org:80
# BioMart database: ENSEMBL_MART_ENSEMBL
# BioMart database version: Ensembl Genes 94
# BioMart dataset: hsapiens_gene_ensembl
# BioMart dataset description: Human genes (GRCh38.p12)
# BioMart dataset version: GRCh38.p12
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 227492
# exon_nrow: 771727
# cds_nrow: 303052
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2018-10-17 15:54:26 +0200 (Wed, 17 Oct 2018)
# GenomicFeatures version at creation time: 1.32.2
# RSQLite version at creation time: 2.1.1
# DBSCHEMAVERSION: 1.2
ADD REPLYlink written 4 weeks ago by Mike Smith3.1k

It is indeed. 

I tried it on a number of different computers and it is happening regardless. It gives me a time-out error in RStudio but it looks like it's due to it taking too long to run.

 

I've tried it again today but to no avail!

 

Best,

 

K

ADD REPLYlink written 4 weeks ago by katie_emelianova0

Update:

I just cleared my R session and restarted everything and it is now working. Sorry!

Perhaps it was something to do with it cacheing or saving data from previous runs.

 

ADD REPLYlink written 4 weeks ago by katie_emelianova0
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