Hello
I'm trying to investigate my Tophat 2.05 Bowtie 2.0 aligned BAM file, plus BAM bai file and cuffdiff 2.02 outputs using the latest version of cummeRbund in R version 2.15.2.
While generating the database using the > cuff <- readCufflinks(rebuild=T) command i encounted an error. Does anyone know what could have caused it?
Any feedback greatfully received
[dr_richard_barker@vm142-21 cuffdiff_out]$ R
R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-redhat-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.
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.
> library (cummeRbund)
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following object(s) are masked from 'package:stats':
xtabs
The following object(s) are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
rownames, sapply, setdiff, table, tapply, union, unique
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(s) are masked from 'package:stats':
hclust
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: IRanges
Loading required package: Gviz
Loading required package: grid
> cuff <- readCufflinks()
> cuff <- readCufflinks(rebuild=T)
Creating database /mydata2/0_GS_atmosphere_test/cuffdiff_out/cuffData.db
Reading Run Info File /mydata2/0_GS_atmosphere_test/cuffdiff_out/run.info
Writing runInfo Table
Reading Read Group Info /mydata2/0_GS_atmosphere_test/cuffdiff_out/read_groups.info
Writing replicates Table
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (RS_SQLite_exec: could not execute: column rep_name is not unique)
>
I'm trying to investigate my Tophat 2.05 Bowtie 2.0 aligned BAM file, plus BAM bai file and cuffdiff 2.02 outputs using the latest version of cummeRbund in R version 2.15.2.
While generating the database using the > cuff <- readCufflinks(rebuild=T) command i encounted an error. Does anyone know what could have caused it?
Any feedback greatfully received
[dr_richard_barker@vm142-21 cuffdiff_out]$ R
R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-redhat-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.
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.
> library (cummeRbund)
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following object(s) are masked from 'package:stats':
xtabs
The following object(s) are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
rownames, sapply, setdiff, table, tapply, union, unique
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(s) are masked from 'package:stats':
hclust
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: IRanges
Loading required package: Gviz
Loading required package: grid
> cuff <- readCufflinks()
> cuff <- readCufflinks(rebuild=T)
Creating database /mydata2/0_GS_atmosphere_test/cuffdiff_out/cuffData.db
Reading Run Info File /mydata2/0_GS_atmosphere_test/cuffdiff_out/run.info
Writing runInfo Table
Reading Read Group Info /mydata2/0_GS_atmosphere_test/cuffdiff_out/read_groups.info
Writing replicates Table
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (RS_SQLite_exec: could not execute: column rep_name is not unique)
>
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