Error with makeTxDbFromBiomart
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sjmonkley ▴ 30
@sjmonkley-8860
Last seen 5 weeks ago
Sweden

I am trying to run makeTxDbFromBiomart as part of a DEXseq analysis but always get the error below:

   > hse = makeTxDbFromBiomart( biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="www.ensembl.org" )
    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 .Ensembl_getMySQLCoreDir(dataset, release = release, use.grch37 = use.grch37,  : 
      found 0 or more than 1 subdir for "hsapiens_gene_ensembl" dataset at ftp://ftp.ensembl.org/pub/release-99/mysql/


> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /opt/scp/software/mro/3.5.1-foss-2017a/lib64/R/lib/libRblas.so
LAPACK: /opt/scp/software/mro/3.5.1-foss-2017a/lib64/R/lib/libRlapack.so

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    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] biomaRt_2.38.0              GenomicFeatures_1.34.8      Rsamtools_1.34.1            Biostrings_2.50.2           XVector_0.22.0              SummarizedExperiment_1.12.0
 [7] DelayedArray_0.8.0          BiocParallel_1.16.6         matrixStats_0.56.0          AnnotationDbi_1.44.0        Biobase_2.42.0              GenomicRanges_1.34.0       
[13] GenomeInfoDb_1.18.2         IRanges_2.16.0              S4Vectors_0.20.1            BiocGenerics_0.28.0         RevoUtils_11.0.1            RevoUtilsMath_11.0.0       

loaded via a namespace (and not attached):
 [1] progress_1.2.0           lattice_0.20-35          vctrs_0.2.4              rtracklayer_1.42.2       yaml_2.2.1               blob_1.2.1              
 [7] XML_3.99-0.3             rlang_0.4.5              DBI_1.1.0                bit64_0.9-7              GenomeInfoDbData_1.2.0   stringr_1.4.0           
[13] zlibbioc_1.28.0          memoise_1.1.0            curl_4.3                 Rcpp_1.0.4.6             BiocManager_1.30.10      bit_1.1-15.2            
[19] hms_0.5.3                digest_0.6.25            stringi_1.4.6            grid_3.5.1               tools_3.5.1              bitops_1.0-6            
[25] magrittr_1.5             RCurl_1.98-1.2           RSQLite_2.2.0            crayon_1.3.4             pkgconfig_2.0.1          Matrix_1.2-11           
[31] prettyunits_1.0.2        assertthat_0.2.0         httr_1.3.1               rstudioapi_0.7           R6_2.2.2                 GenomicAlignments_1.18.1
[37] compiler_3.5.1          
GenomicFeatures • 259 views
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@james-w-macdonald-5106
Last seen 16 hours ago
United States

You are using an old (unsupported) version of R/BioC. At the very least you need to upgrade to the current release version, which uses R-3.6.x. But there is a new version of BioC set to be released tomorrow, so you should probably get ahead of the game and install R-4.0.0 and the devel (which will be release tomorrow) version of Bioconductor.

If the updated version of R/BioC still doesn't work, let us know.

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OK thanks. I am somewhat restricted with R versions if use RStudio on our scp but will need to find another way then.

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