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  • CummerBund database problem

    Hello,

    I'm using Rstudio to run cummerBund on my RNA-seq results. I've done this before and it has worked beautifully. Recently I updated to Mac OS X yosemite and now I can't make the cufflinks database. I keep getting this error:

    > cuff_data<-readCufflinks("diff_out")
    Creating database diff_out/cuffData.db
    Error in .local(drv, ...) : Could not connect to database:
    unable to open database file

    I've updated Rstudio and R to the most current versions but I'm still getting this error. Is anyone else having a similar problem?

  • #2
    Here is the download info for the this problem:

    R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
    Copyright (C) 2015 The R Foundation for Statistical Computing
    Platform: x86_64-apple-darwin13.4.0 (64-bit)

    R is free software and comes with ABSOLUTELY NO WARRANTY.
    You are welcome to redistribute it under certain conditions.
    Type 'license()' or 'licence()' for distribution details.

    Natural language support but running in an English locale

    R is a collaborative project with many contributors.
    Type 'contributors()' for more information and
    'citation()' on how to cite R or R packages in publications.

    Type 'demo()' for some demos, 'help()' for on-line help, or
    'help.start()' for an HTML browser interface to help.
    Type 'q()' to quit R.

    > source("http://bioconductor.org/biocLite.R")
    Bioconductor version 3.1 (BiocInstaller 1.18.2), ?biocLite for help
    > biocLite("cummeRbund")
    BioC_mirror: http://bioconductor.org
    Using Bioconductor version 3.1 (BiocInstaller 1.18.2), R version 3.2.0.
    Installing package(s) ‘cummeRbund’
    trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/macosx/mavericks/contrib/3.2/cummeRbund_2.10.0.tgz'
    Content type 'application/x-gzip' length 2567027 bytes (2.4 MB)
    ==================================================
    downloaded 2.4 MB


    The downloaded binary packages are in
    /var/folders/34/9_xs5yk16p74j3d8fdf92q_00000gn/T//Rtmprt7bu5/downloaded_packages
    > getwd()
    [1] "/Users/John"
    > setwd("/Users/John/Documents/Tabin_Lab/Skeleton/A-P_Cuffdiff_files/Ant_v_Pos/")
    > getwd()
    [1] "/Users/John/Documents/Tabin_Lab/Skeleton/A-P_Cuffdiff_files/Ant_v_Pos"
    > library(cummeRbund)
    Loading required package: BiocGenerics
    Loading required package: parallel

    Attaching package: ‘BiocGenerics’

    The following objects are masked from ‘packagearallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

    The following object is masked from ‘package:stats’:

    xtabs

    The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind,
    colnames, do.call, duplicated, eval, evalq, Filter, Find,
    get, intersect, is.unsorted, lapply, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rep.int, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist,
    unsplit

    Loading required package: RSQLite
    Loading required package: DBI
    Loading required package: ggplot2
    Loading required package: reshape2
    Loading required package: fastcluster

    Attaching package: ‘fastcluster’

    The following object is masked from ‘package:stats’:

    hclust

    Loading required package: rtracklayer
    Loading required package: GenomicRanges
    Loading required package: S4Vectors
    Loading required package: stats4
    Loading required package: IRanges
    Loading required package: GenomeInfoDb
    Loading required package: Gviz
    Loading required package: grid

    Attaching package: ‘cummeRbund’

    The following object is masked from ‘package:GenomicRanges’:

    promoters

    The following object is masked from ‘package:IRanges’:

    promoters

    The following object is masked from ‘package:BiocGenerics’:

    conditions

    > cuff_data<-readCufflinks("diff_out")
    Creating database diff_out/cuffData.db
    Error in .local(drv, ...) : Could not connect to database:
    unable to open database file
    >

    Can anyone tell me what I'm doing wrong?

    Comment


    • #3
      And here is the session info:
      R version 3.2.0 (2015-04-16)
      Platform: x86_64-apple-darwin13.4.0 (64-bit)
      Running under: OS X 10.10.3 (Yosemite)

      locale:
      [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

      other attached packages:
      [1] cummeRbund_2.10.0 Gviz_1.12.0 rtracklayer_1.28.4
      [4] GenomicRanges_1.20.4 GenomeInfoDb_1.4.0 IRanges_2.2.3
      [7] S4Vectors_0.6.0 fastcluster_1.1.16 reshape2_1.4.1
      [10] ggplot2_1.0.1 RSQLite_1.0.0 DBI_0.3.1
      [13] BiocGenerics_0.14.0 BiocInstaller_1.18.2

      loaded via a namespace (and not attached):
      [1] Rcpp_0.11.6 RColorBrewer_1.1-2
      [3] futile.logger_1.4.1 plyr_1.8.2
      [5] XVector_0.8.0 GenomicFeatures_1.20.1
      [7] bitops_1.0-6 futile.options_1.0.0
      [9] tools_3.2.0 zlibbioc_1.14.0
      [11] rpart_4.1-9 biomaRt_2.24.0
      [13] digest_0.6.8 BSgenome_1.36.0
      [15] biovizBase_1.16.0 lattice_0.20-31
      [17] gtable_0.1.2 proto_0.3-10
      [19] gridExtra_0.9.1 cluster_2.0.1
      [21] stringr_1.0.0 Biostrings_2.36.1
      [23] nnet_7.3-9 Biobase_2.28.0
      [25] AnnotationDbi_1.30.1 survival_2.38-1
      [27] XML_3.98-1.2 BiocParallel_1.2.2
      [29] foreign_0.8-63 Formula_1.2-1
      [31] latticeExtra_0.6-26 lambda.r_1.1.7
      [33] magrittr_1.5 splines_3.2.0
      [35] Hmisc_3.16-0 matrixStats_0.14.0
      [37] scales_0.2.4 Rsamtools_1.20.4
      [39] MASS_7.3-40 GenomicAlignments_1.4.1
      [41] dichromat_2.0-0 colorspace_1.2-6
      [43] stringi_0.4-1 acepack_1.3-3.3
      [45] RCurl_1.95-4.6 munsell_0.4.2
      [47] VariantAnnotation_1.14.1
      >

      Again, any help is greatly appreciated!

      Comment


      • #4
        Since no one has responded so far I will offer a suggestion to try based on this post (https://support.bioconductor.org/p/46507/).

        Have you tried to provide full path to the "diff_out" directory?

        This thread has some additional info: http://seqanswers.com/forums/showthread.php?t=47982

        Comment


        • #5
          Thanks, I was able to get it to work by providing the full path but not including "diff_out"

          Thank you for your help!

          J

          Comment


          • #6
            I'm having the same problem with cummRbund..
            could anybody help me?
            R version 3.2.4 Revised (2016-03-16 r70336) -- "Very Secure Dishes"
            Copyright (C) 2016 The R Foundation for Statistical Computing
            Platform: x86_64-pc-linux-gnu (64-bit)

            R é um software livre e vem sem GARANTIA ALGUMA.
            Você pode redistribuí-lo sob certas circunstâncias.
            Digite 'license()' ou 'licence()' para detalhes de distribuição.

            R é um projeto colaborativo com muitos contribuidores.
            Digite 'contributors()' para obter mais informações e
            'citation()' para saber como citar o R ou pacotes do R em publicações.

            Digite 'demo()' para demonstrações, 'help()' para o sistema on-line de ajuda,
            ou 'help.start()' para abrir o sistema de ajuda em HTML no seu navegador.
            Digite 'q()' para sair do R.

            > library(cummeRbund)
            Carregando pacotes exigidos: BiocGenerics
            Carregando pacotes exigidos: parallel

            Attaching package: ‘BiocGenerics’

            The following objects are masked from ‘packagearallel’:

            clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
            clusterExport, clusterMap, parApply, parCapply, parLapply,
            parLapplyLB, parRapply, parSapply, parSapplyLB

            The following objects are masked from ‘package:stats’:

            IQR, mad, xtabs

            The following objects are masked from ‘package:base’:

            anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
            do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
            intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
            order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
            rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
            union, unique, unlist, unsplit

            Carregando pacotes exigidos: RSQLite
            Carregando pacotes exigidos: DBI
            Carregando pacotes exigidos: ggplot2
            Carregando pacotes exigidos: reshape2
            Carregando pacotes exigidos: fastcluster

            Attaching package: ‘fastcluster’

            The following object is masked from ‘package:stats’:

            hclust

            Carregando pacotes exigidos: rtracklayer
            Carregando pacotes exigidos: GenomicRanges
            Carregando pacotes exigidos: S4Vectors
            Carregando pacotes exigidos: stats4
            Carregando pacotes exigidos: IRanges
            Carregando pacotes exigidos: GenomeInfoDb
            Carregando pacotes exigidos: Gviz
            Carregando pacotes exigidos: grid

            Attaching package: ‘cummeRbund’

            The following object is masked from ‘package:GenomicRanges’:

            promoters

            The following object is masked from ‘package:IRanges’:

            promoters

            The following object is masked from ‘package:BiocGenerics’:

            conditions

            > > cuff_data <- readCufflinks('diff_out')
            Erro: '>' inesperado in " >"
            > cuff_data <- readCufflinks('diff_out')
            Creating database diff_out/cuffData.db
            Error in .local(drv, ...) : Could not connect to database:
            unable to open database file

            Comment


            • #7
              ANSWER: Solution to Database connection error in cummeRbund.

              Enter into R
              $R
              R version 3.5.1 (2018-07-02) -- "Feather Spray"
              Copyright (C) 2018 The R Foundation for Statistical Computing
              Platform: x86_64-pc-linux-gnu (64-bit)

              R is free software and comes with ABSOLUTELY NO WARRANTY.
              You are welcome to redistribute it under certain conditions.
              Type 'license()' or 'licence()' for distribution details.

              Natural language support but running in an English locale

              R is a collaborative project with many contributors.
              Type 'contributors()' for more information and
              'citation()' on how to cite R or R packages in publications.

              Type 'demo()' for some demos, 'help()' for on-line help, or
              'help.start()' for an HTML browser interface to help.
              Type 'q()' to quit R.
              >

              Now keep the cuffdiff output in Desktop (Linux). Suppose CuffDiff output folder is dge-result.
              >setwd(~/Desktop/dge-result)
              >getwd()
              Load cummeRbund and RSQLite
              >library("cummeRbund")
              >library(RSQLite)
              >cuff<-readCufflinks("~/Desktop/dge-result")
              Creating database ~/Desktop/dge-result/cuffData.db
              Reading Run Info File ~/Desktop/dge-result/run.info
              Writing runInfo Table
              Reading Read Group Info ~/Desktop/dge-result/read_groups.info
              Writing replicates Table
              Reading Var Model Info ~/Desktop/dge-result/var_model.info
              Writing varModel Table
              Reading ~/Desktop/dge-result/genes.fpkm_tracking
              Checking samples table...
              Populating samples table...
              Writing genes table
              Reshaping geneData table
              Recasting
              Writing geneData table
              Reading ~/Desktop/dge-result/gene_exp.diff
              Writing geneExpDiffData table
              Reading ~/Desktop/dge-result/promoters.diff
              Writing promoterDiffData table
              Reading ~/Desktop/dge-result/genes.count_tracking
              Reshaping geneCount table
              Recasting
              Writing geneCount table
              Reading read group info in ~/Desktop/dge-result/genes.read_group_tracking
              Writing geneReplicateData table
              Reading ~/Desktop/dge-result/isoforms.fpkm_tracking
              Checking samples table...
              OK!
              Writing isoforms table
              Reshaping isoformData table
              Recasting
              Writing isoformData table
              Reading ~/Desktop/dge-result/isoform_exp.diff
              Writing isoformExpDiffData table
              Reading ~/Desktop/dge-result/isoforms.count_tracking
              Reshaping isoformCount table
              Recasting
              Writing isoformCount table
              Reading read group info in ~/Desktop/dge-result/isoforms.read_group_tracking
              Writing isoformReplicateData table
              Reading ~/Desktop/dge-result/tss_groups.fpkm_tracking
              Checking samples table...
              OK!
              Writing TSS table
              Reshaping TSSData table
              Recasting
              Writing TSSData table
              Reading ~/Desktop/dge-result/tss_group_exp.diff
              Writing TSSExpDiffData table
              Reading ~/Desktop/dge-result/splicing.diff
              Writing splicingDiffData table
              Reading ~/Desktop/dge-result/tss_groups.count_tracking
              Reshaping TSSCount table
              Recasting
              Writing TSSCount table
              Reading read group info in ~/Desktop/dge-result/tss_groups.read_group_tracking
              Writing TSSReplicateData table
              Reading ~/Desktop/dge-result/cds.fpkm_tracking
              Checking samples table...
              OK!
              Writing CDS table
              No records found in ~/Desktop/dge-result/cds.fpkm_tracking
              CDS FPKM tracking file was empty.
              Reading ~/Desktop/dge-result/cds_exp.diff
              No records found in ~/Desktop/dge-result/cds_exp.diff
              Reading ~/Desktop/dge-result/cds.diff
              No records found in ~/Desktop/dge-result/cds.diff
              Reading ~/Desktop/dge-result/cds.count_tracking
              No records found in ~/Desktop/dge-result/cds.count_tracking
              Reading read group info in ~/Desktop/dge-result/cds.read_group_tracking
              No records found in ~/Desktop/dge-result/cds.read_group_tracking
              Indexing Tables...
              There were 50 or more warnings (use warnings() to see the first 50)
              > cuff
              CuffSet instance with:
              2 samples
              23363 genes
              37735 isoforms
              27162 TSS
              0 CDS
              23363 promoters
              27162 splicing
              0 relCDS
              > Check the dge-result directory , you will get a file CuffData.db

              Comment

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