cummeRbund readCufflinks Error in sqliteSendQuery

[Pinal]

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?

[Frithjof]

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

[Frithjof]

Solved:

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