Question: Problem with RIPSeeker
1
gravatar for Nicola Cole
6.3 years ago by
Nicola Cole30
Nicola Cole30 wrote:
Hi, I am trying to use RIPSeeker with bam files generated from Arabidopsis. I have emailed the author numerous times, and she has finally referred me to you all. The error I am getting is: Error in useMart(dataset = biomaRt_dataset, ...) : Incorrect BioMart name, use the listMarts function to see which BioMart databases are available Calls: ripSeek ... suppressMessages -> withCallingHandlers -> annotateRIP -> useMart Execution halted The script I am using is: #!/bin/bash source("http://bioconductor.org/biocLite.R") biocLite("RIPSeeker") library(RIPSeeker) biocLite("biomaRt") library(biomaRt) biocLite("ChIPpeakAnno") biocLite("GenomicFeatures") library(GenomicFeatures) library(GenomicRanges) library(rtracklayer) bamFiles<-list.files("/work/02044/ncole/Anna_Analysis/Bam_Files_for_RI PSeek/Temp_Bam_Files/","\\.bam$", recursive=TRUE, full.names=TRUE) cName <- "Control_ " outDir<-file.path(getwd(),"Nicola_4G_out") binSize<-NULL minBinSize <- 10000 maxBinSize <- 10100 multicore <- TRUE strandType <-NULL biomart <- "ENSEMBL_MART_PLANT" biomaRt_dataset <- "athaliana_eg_gene" goAnno <- "org.At.tair.db" seekOut.All_the_bams<- ripSeek(bamPath = bamFiles, cName = cName, reverseComplement = TRUE,strandType = strandType, uniqueHit = TRUE, assignMultihits = TRUE, rerunWithDisambiguatedMultihits = TRUE, binSize=binSize, minBinSize = minBinSize, maxBinSize = maxBinSize, biomart=biomart, biomaRt_dataset = biomaRt_dataset, goAnno = goAnno, multicore=multicore, outDir=outDir) q() While "ENSEMBL_MART_PLANT" comes up in the listMarts function when I try to use that in the useMart function, I get the error: Error in useMart(ENSEMBL_MART_PLANT, dataset, host = "www.biomart.org", : object 'ENSEMBL_MART_PLANT' not found Can you tell me what needs changing in my script? Thank you, Nicola Cole Browning Lab PhD candidate UT Ausitn
biomart ripseeker • 1.3k views
ADD COMMENTlink modified 6.3 years ago by António Miguel de Jesus Domingues470 • written 6.3 years ago by Nicola Cole30
Answer: Problem with RIPSeeker
0
gravatar for Nicola Cole
6.3 years ago by
Nicola Cole30
Nicola Cole30 wrote:
Hi, It finally worked for me. Nicola On Aug 15, 2013, at 11:00 AM, Nicola Cole <ncole at="" utexas.edu=""> wrote: > Hi, > > I am trying to use RIPSeeker with bam files generated from Arabidopsis. I have emailed the author numerous times, and she has finally referred me to you all. > > The error I am getting is: > > Error in useMart(dataset = biomaRt_dataset, ...) : > Incorrect BioMart name, use the listMarts function to see which BioMart databases are available > Calls: ripSeek ... suppressMessages -> withCallingHandlers -> annotateRIP -> useMart > Execution halted > > The script I am using is: > > #!/bin/bash > > source("http://bioconductor.org/biocLite.R") > biocLite("RIPSeeker") > library(RIPSeeker) > biocLite("biomaRt") > library(biomaRt) > biocLite("ChIPpeakAnno") > biocLite("GenomicFeatures") > library(GenomicFeatures) > library(GenomicRanges) > library(rtracklayer) > > bamFiles<-list.files("/work/02044/ncole/Anna_Analysis/Bam_Files_for_ RIPSeek/Temp_Bam_Files/","\\.bam$", > recursive=TRUE, full.names=TRUE) > cName <- "Control_ " > outDir<-file.path(getwd(),"Nicola_4G_out") > binSize<-NULL > minBinSize <- 10000 > maxBinSize <- 10100 > multicore <- TRUE > strandType <-NULL > biomart <- "ENSEMBL_MART_PLANT" > biomaRt_dataset <- "athaliana_eg_gene" > goAnno <- "org.At.tair.db" > > seekOut.All_the_bams<- ripSeek(bamPath = bamFiles, cName = cName, > reverseComplement = TRUE,strandType = strandType, > uniqueHit = TRUE, assignMultihits = TRUE, > rerunWithDisambiguatedMultihits = TRUE, > binSize=binSize, minBinSize = minBinSize, > maxBinSize = maxBinSize, > biomart=biomart, > biomaRt_dataset = biomaRt_dataset, goAnno = goAnno, > multicore=multicore, outDir=outDir) > > q() > > While "ENSEMBL_MART_PLANT" comes up in the listMarts function when I try to use that in the useMart function, I get the error: > > Error in useMart(ENSEMBL_MART_PLANT, dataset, host = "www.biomart.org", : > object 'ENSEMBL_MART_PLANT' not found > > > Can you tell me what needs changing in my script? > > Thank you, > > Nicola Cole > Browning Lab > PhD candidate > UT Ausitn >
ADD COMMENTlink written 6.3 years ago by Nicola Cole30
Hi Nicole, On Thu, Aug 15, 2013 at 7:24 PM, Nicola Cole <ncole at="" utexas.edu=""> wrote: > Hi, > > It finally worked for me. For the benefit of others, can you share with us what the problem that you identified was along with the fix? Thanks, -steve > > Nicola > > > > On Aug 15, 2013, at 11:00 AM, Nicola Cole <ncole at="" utexas.edu=""> wrote: > >> Hi, >> >> I am trying to use RIPSeeker with bam files generated from Arabidopsis. I have emailed the author numerous times, and she has finally referred me to you all. >> >> The error I am getting is: >> >> Error in useMart(dataset = biomaRt_dataset, ...) : >> Incorrect BioMart name, use the listMarts function to see which BioMart databases are available >> Calls: ripSeek ... suppressMessages -> withCallingHandlers -> annotateRIP -> useMart >> Execution halted >> >> The script I am using is: >> >> #!/bin/bash >> >> source("http://bioconductor.org/biocLite.R") >> biocLite("RIPSeeker") >> library(RIPSeeker) >> biocLite("biomaRt") >> library(biomaRt) >> biocLite("ChIPpeakAnno") >> biocLite("GenomicFeatures") >> library(GenomicFeatures) >> library(GenomicRanges) >> library(rtracklayer) >> >> bamFiles<-list.files("/work/02044/ncole/Anna_Analysis/Bam_Files_for _RIPSeek/Temp_Bam_Files/","\\.bam$", >> recursive=TRUE, full.names=TRUE) >> cName <- "Control_ " >> outDir<-file.path(getwd(),"Nicola_4G_out") >> binSize<-NULL >> minBinSize <- 10000 >> maxBinSize <- 10100 >> multicore <- TRUE >> strandType <-NULL >> biomart <- "ENSEMBL_MART_PLANT" >> biomaRt_dataset <- "athaliana_eg_gene" >> goAnno <- "org.At.tair.db" >> >> seekOut.All_the_bams<- ripSeek(bamPath = bamFiles, cName = cName, >> reverseComplement = TRUE,strandType = strandType, >> uniqueHit = TRUE, assignMultihits = TRUE, >> rerunWithDisambiguatedMultihits = TRUE, >> binSize=binSize, minBinSize = minBinSize, >> maxBinSize = maxBinSize, >> biomart=biomart, >> biomaRt_dataset = biomaRt_dataset, goAnno = goAnno, >> multicore=multicore, outDir=outDir) >> >> q() >> >> While "ENSEMBL_MART_PLANT" comes up in the listMarts function when I try to use that in the useMart function, I get the error: >> >> Error in useMart(ENSEMBL_MART_PLANT, dataset, host = "www.biomart.org", : >> object 'ENSEMBL_MART_PLANT' not found >> >> >> Can you tell me what needs changing in my script? >> >> Thank you, >> >> Nicola Cole >> Browning Lab >> PhD candidate >> UT Ausitn >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
ADD REPLYlink written 6.3 years ago by Steve Lianoglou12k
Answer: Problem with RIPSeeker
0
gravatar for António Miguel de Jesus Domingues
6.3 years ago by
Germany
Hi Nicola, is that really the script you are using? Running it from the shell? If so, there is a mistake in the header: > #!/bin/bash will run it as a bash script and not as R. The first line of the file should be: > #! /usr/bin/Rscript --vanilla As for the actual error, which probably came from the R console, I can't help you much there. Best, António On 16/08/13 12:00, bioconductor-request@r-project.org wrote: > On Aug 15, 2013, at 11:00 AM, Nicola Cole<ncole@utexas.edu> wrote: > >> >Hi, >> > >> >I am trying to use RIPSeeker with bam files generated from Arabidopsis. I have emailed the author numerous times, and she has finally referred me to you all. >> > >> >The error I am getting is: >> > >> >Error in useMart(dataset = biomaRt_dataset, ...) : >> > Incorrect BioMart name, use the listMarts function to see which BioMart databases are available >> >Calls: ripSeek ... suppressMessages -> withCallingHandlers -> annotateRIP -> useMart >> >Execution halted >> > >> >The script I am using is: >> > >> >#!/bin/bash >> > >> >source("http://bioconductor.org/biocLite.R") >> >biocLite("RIPSeeker") >> >library(RIPSeeker) >> >biocLite("biomaRt") >> >library(biomaRt) >> >biocLite("ChIPpeakAnno") >> >biocLite("GenomicFeatures") >> >library(GenomicFeatures) >> >library(GenomicRanges) >> >library(rtracklayer) >> > >> >bamFiles<-list.files("/work/02044/ncole/Anna_Analysis/Bam_Files_fo r_RIPSeek/Temp_Bam_Files/","\\.bam$", >> >recursive=TRUE, full.names=TRUE) >> >cName <- "Control_ " >> >outDir<-file.path(getwd(),"Nicola_4G_out") >> >binSize<-NULL >> >minBinSize <- 10000 >> >maxBinSize <- 10100 >> >multicore <- TRUE >> >strandType <-NULL >> >biomart <- "ENSEMBL_MART_PLANT" >> >biomaRt_dataset <- "athaliana_eg_gene" >> >goAnno <- "org.At.tair.db" >> > >> >seekOut.All_the_bams<- ripSeek(bamPath = bamFiles, cName = cName, >> >reverseComplement = TRUE,strandType = strandType, >> >uniqueHit = TRUE, assignMultihits = TRUE, >> >rerunWithDisambiguatedMultihits = TRUE, >> >binSize=binSize, minBinSize = minBinSize, >> >maxBinSize = maxBinSize, >> >biomart=biomart, >> >biomaRt_dataset = biomaRt_dataset, goAnno = goAnno, >> >multicore=multicore, outDir=outDir) >> > >> >q() >> > >> >While "ENSEMBL_MART_PLANT" comes up in the listMarts function when I try to use that in the useMart function, I get the error: >> > >> >Error in useMart(ENSEMBL_MART_PLANT, dataset, host = "www.biomart.org", : >> > object 'ENSEMBL_MART_PLANT' not found >> > >> > >> >Can you tell me what needs changing in my script? >> > >> >Thank you, >> > >> >Nicola Cole >> >Browning Lab >> >PhD candidate >> >UT Ausitn >> > -- António Miguel de Jesus Domingues, PhD Neugebauer group Max Planck Institute of Molecular Cell Biology and Genetics, Dresden Pfotenhauerstrasse 108 01307 Dresden Germany e-mail: domingue@mpi-cbg.de tel. +49 351 210 2481 The Unbearable Lightness of Molecular Biology [[alternative HTML version deleted]]
ADD COMMENTlink written 6.3 years ago by António Miguel de Jesus Domingues470
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