Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • cummeRbund readCufflinks Error in sqliteSendQuery

    Dear All,

    When using library cummeRbund with readCufflinks, I got errors:


    Creating database /home/NGS/diff_out/cuffData.db
    Reading Run Info File /home/NGS/diff_out/run.info
    Writing runInfo Table
    Reading Read Group Info /home/NGS/diff_out/read_groups.info
    Writing replicates Table
    Error in sqliteSendQuery(con, statement, bind.data) :
    rsqlite_query_send: could not execute: UNIQUE constraint failed: replicates.rep_name

    I tried a alot but could not find any solution. Could you please give me some suggestions?

  • #2
    Dear all,

    I am having the same problem. Does it relate to the names/labels of the samples ?

    Any help is highly appreciated.

    Best,
    Frithjof

    > cuff <- readCufflinks(dir = getwd(),gtfFile="cufflinks/cuffmerge/cufflinks_mapping/merged.gtf",genome="mm10",rebuild=T)
    Creating database cufflinks/cuffdiff/cufflinks_mapping_neu/cuffData.db
    Reading Run Info File cufflinks/cuffdiff/cufflinks_mapping_neu/run.info
    Writing runInfo Table
    Reading Read Group Info cufflinks/cuffdiff/cufflinks_mapping_neu/read_groups.info
    Writing replicates Table
    Error in sqliteSendQuery(con, statement, bind.data) :
    rsqlite_query_send: could not execute: UNIQUE constraint failed: replicates.rep_name


    > sessionInfo()
    R version 3.3.0 (2016-05-03)
    Platform: x86_64-pc-linux-gnu (64-bit)
    Running under: Ubuntu 14.04.4 LTS

    locale:
    [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 LC_MONETARY=de_DE.UTF-8
    [6] LC_MESSAGES=de_DE.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
    [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

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

    other attached packages:
    [1] cummeRbund_2.14.0 Gviz_1.16.1 rtracklayer_1.32.1 GenomicRanges_1.24.1 GenomeInfoDb_1.8.1 IRanges_2.6.0
    [7] S4Vectors_0.10.1 fastcluster_1.1.20 reshape2_1.4.1 ggplot2_2.1.0 RSQLite_1.0.0 DBI_0.4-1
    [13] BiocGenerics_0.18.0

    loaded via a namespace (and not attached):
    [1] SummarizedExperiment_1.2.3 VariantAnnotation_1.18.1 splines_3.3.0 lattice_0.20-33
    [5] colorspace_1.2-6 htmltools_0.3.5 GenomicFeatures_1.24.2 chron_2.3-47
    [9] interactiveDisplayBase_1.10.3 XML_3.98-1.4 survival_2.39-4 foreign_0.8-66
    [13] ensembldb_1.4.6 BiocParallel_1.6.2 RColorBrewer_1.1-2 matrixStats_0.50.2
    [17] plyr_1.8.4 stringr_1.0.0 zlibbioc_1.18.0 Biostrings_2.40.2
    [21] munsell_0.4.3 gtable_0.2.0 latticeExtra_0.6-28 Biobase_2.32.0
    [25] biomaRt_2.28.0 BiocInstaller_1.22.2 httpuv_1.3.3 AnnotationDbi_1.34.3
    [29] Rcpp_0.12.5 xtable_1.8-2 acepack_1.3-3.3 BSgenome_1.40.0
    [33] scales_0.4.0 Hmisc_3.17-4 XVector_0.12.0 mime_0.4
    [37] Rsamtools_1.24.0 gridExtra_2.2.1 AnnotationHub_2.4.2 digest_0.6.9
    [41] stringi_1.1.1 biovizBase_1.20.0 shiny_0.13.2 tools_3.3.0
    [45] bitops_1.0-6 magrittr_1.5 RCurl_1.95-4.8 dichromat_2.0-0
    [49] Formula_1.2-1 cluster_2.0.4 Matrix_1.2-6 data.table_1.9.6
    [53] httr_1.2.0 R6_2.1.2 rpart_4.1-10 GenomicAlignments_1.8.1
    [57] nnet_7.3-12



    read_groups.info contains
    file condition replicate_num total_mass norm_mass internal_scale external_scale
    /cufflinks_mapping/accepted_hits_mESC_1_sorted.bam mESC 0 2.54663e+07 2.44193e+07 1.00186 1
    /cufflinks_mapping/accepted_hits_mESC_2_sorted.bam mESC 1 2.2835e+07 2.44193e+07 0.916723 1
    /cufflinks_mapping/accepted_hits_mESC_3_sorted.bam mESC 2 2.56382e+07 2.44193e+07 0.990362 1
    /cufflinks_mapping/accepted_hits_d4.75_both_1_sorted.bam d4.75_both 0 2.59334e+07 2.44193e+07 1.08512 1
    /cufflinks_mapping/accepted_hits_d4.75_both_2_sorted.bam d4.75_both 1 2.58051e+07 2.44193e+07 1.08307 1
    /cufflinks_mapping/accepted_hits_d4.75_both_3_sorted.bam d4.75_both 2 2.70496e+07 2.44193e+07 1.13197 1
    /cufflinks_mapping/accepted_hits_d4.75_GFP+_1_sorted.bam d4.75_GFP+ 0 2.8343e+07 2.44193e+07 1.17596 1
    /cufflinks_mapping/accepted_hits_d4.75_GFP+_2_sorted.bam d4.75_GFP+ 1 2.81964e+07 2.44193e+07 1.15372 1
    /cufflinks_mapping/accepted_hits_d4.75_GFP+_3_sorted.bam d4.75_GFP+ 2 2.14949e+07 2.44193e+07 0.864442 1
    /cufflinks_mapping/accepted_hits_d4.75_GFP-_1_sorted.bam d4.75_GFP- 0 2.30895e+07 2.44193e+07 0.964971 1
    /cufflinks_mapping/accepted_hits_d4.75_GFP-_2_sorted.bam d4.75_GFP- 1 1.98995e+07 2.44193e+07 0.83213 1
    /cufflinks_mapping/accepted_hits_d4.75_GFP-_3_sorted.bam d4.75_GFP- 2 2.34407e+07 2.44193e+07 0.978108 1
    Last edited by Frithjof; 06-16-2016, 02:29 AM.

    Comment


    • #3
      Solved:

      Solved this by removing all special characters from sample names and labels.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM
      • seqadmin
        The Impact of AI in Genomic Medicine
        by seqadmin



        Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
        02-26-2024, 02:07 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 03-14-2024, 06:13 AM
      0 responses
      34 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-08-2024, 08:03 AM
      0 responses
      72 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-07-2024, 08:13 AM
      0 responses
      81 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-06-2024, 09:51 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X