Question: Update database names in the biomaRT package
gravatar for aspadotto
4.7 years ago by
aspadotto20 wrote:

Hi all!


When running RIPseeker in the last days, using this command

R '--no-save --args trtbam=/projects/igats/RIPseq/2015/2015-01-Tell-RIPseq/IP-resina/IP-resina/accepted_hits_selected.bam ctrbam=/projects/igats/RIPseq/2015/2015-01-Tell-RIPseq/INPUT-resina/INPUT-resina/accepted_hits_selected.bam cNAME=/projects/igats/RIPseq/2015/2015-01-Tell-RIPseq/INPUT-resina/INPUT-resina/accepted_hits outfile=IP-resina_vs_INPUT-resina.csv ripseekoutdir=./ paired=n multicore=y binSize=1000 biomart=ensembl biomaRt_dataset=hsapiens_gene_ensembl minBinSize=NULL maxBinSize=NULL strandType=NULL genomeBuild=hg19' < /projects/igats/RIPseq/2014/2014-06_Damante_Puppin_RIP-seq/09062014_new_test/workflow_RIPseq.r log.out 2> log.err


and obtaining this error log


Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help
A newer version of Bioconductor is available after installing a new version of
  R, ?BiocUpgrade for help
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

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

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


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

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

Loading required package: GenomicRanges
Loading required package: XVector
Loading required package: rtracklayer
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: grid
Loading required package: VennDiagram
Loading required package: multtest
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: BSgenome
Loading required package: BSgenome.Ecoli.NCBI.20080805
Loading required package: GO.db
Loading required package: AnnotationDbi

Attaching package: ‘AnnotationDbi’

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


Loading required package: DBI

Loading required package:

Loading required package: limma

Attaching package: ‘limma’

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


Loading required package: GenomicFeatures

*I. Collect alignment files

RIP alignment files:

Control alignment files:


*II. Analyzing RIP library:

**A. Process and combine alignment files

Processing /projects/igats/RIPseq/2015/2015-01-Tell-RIPseq/IP-resina/IP-resina/accepted_hits_selected.bam ... 
Execution halted

We've discovered that the database names are changed, while in the biomaRT package they did not update those names...


Can anyone please help us?


biomart database • 685 views
ADD COMMENTlink modified 4.7 years ago by Julian Gehring1.3k • written 4.7 years ago by aspadotto20
Answer: Update database names in the biomaRT package
gravatar for Julian Gehring
4.7 years ago by
Julian Gehring1.3k
Julian Gehring1.3k wrote:

Your are running an old, unmaintained version of Bioconductor (current is 3.0) and hence of the biomaRt package. An upgrade may fix your problem. In any way, without the actual code (i.e. the content of the script file) it will be hard to diagnose the problem.

ADD COMMENTlink written 4.7 years ago by Julian Gehring1.3k
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