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 goAnno=org.Hs.eg.db 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’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
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
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’:
species
Loading required package: DBI
Loading required package: org.Hs.eg.db
Loading required package: limma
Attaching package: ‘limma’
The following object is masked from ‘package:BiocGenerics’:
plotMA
Loading required package: GenomicFeatures
*I. Collect alignment files
RIP alignment files:
/projects/igats/RIPseq/2015/2015-01-Tell-RIPseq/IP-resina/IP-resina/accepted_hits_selected.bam
Control alignment files:
/projects/igats/RIPseq/2015/2015-01-Tell-RIPseq/INPUT-resina/INPUT-resina/accepted_hits_selected.bam
*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?
