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Old 06-03-2015, 12:19 PM   #1
jyoung528
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Default 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?
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Old 06-04-2015, 07:04 AM   #2
jyoung528
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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?
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Old 06-04-2015, 10:09 AM   #3
jyoung528
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Default

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!
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Old 06-04-2015, 11:01 AM   #4
GenoMax
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Default

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
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Old 06-06-2015, 05:32 PM   #5
jyoung528
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Default

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
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Old 05-06-2016, 11:33 AM   #6
luana
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Default

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
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Old 11-05-2018, 02:02 AM   #7
Ranjan Jyoti Sarma
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Location: Mizoram, India

Join Date: Nov 2018
Posts: 1
Smile 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
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