[Bioc-sig-seq] scanBam Error
Dario Strbenac
D.Strbenac at garvan.org.au
Mon Dec 13 23:00:37 CET 2010
Hi,
Yes, that works fine, thanks. It must've been a size issue I was having.
---- Original message ----
>Date: Mon, 13 Dec 2010 17:31:24 +1000
>From: Paul Leo <p.leo at uq.edu.au>
>Subject: Re: [Bioc-sig-seq] scanBam Error
>To: D.Strbenac at garvan.org.au
>Cc: bioc-sig-sequencing at r-project.org
>
> Do you need all the sequence data at once?
>
> Instead of using a smaller bam file can you read in
> a smaller portion of your large bamfile ?
>
> data.gr<-GRanges(seqnames
> =paste("chr",13,sep=""),ranges =
> IRanges(start=as.numeric(28608234),end=as.numeric(28608363)),strand="+")
>
> which<- data.gr
> params<-ScanBamParam(which=which,flag=scanBamFlag(isUnmappedQuery=FALSE,isDuplicate=NA,isValidVendorRead=TRUE),simpleCigar
> = FALSE,reverseComplement =
> FALSE,what=c("qname","flag","rname","seq","strand","pos","mpos","qwidth","cigar","qual","mapq","isize",
> "mrnm" ),tag="RG" ) # change to what you want
> aln1 <- scanBam("HS1808.bam",param=params)
>
> aln1[[1]]
>
> That should work fine?
>
>--
>Dr Paul Leo
>Bioinformatician
>UQ Diamantina Institute for Cancer, Immunology and Metabolic Medicine
>---------------------------------------------------------------------
>Level 4, R Wing
>Princess Alexandra Hospital
>Ipswich Rd
>Woolloongabba QLD 4102
>Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946
>Email: p.leo at uq.edu.au Web: http://www.di.uq.edu.au
>
> -----Original Message-----
> From: Dario Strbenac <D.Strbenac at garvan.org.au>
> Reply-to: D.Strbenac at garvan.org.au
> To: bioc-sig-sequencing at r-project.org
> Subject: Re: [Bioc-sig-seq] scanBam Error
> Date: Mon, 13 Dec 2010 17:15:38 +1100
>
> I tried it out by making a smaller bam file with only reads from one chromosome, and it worked fine. The full bam file is 4 GB and has 75 million reads in it. Could the size be a problem ? Could you test out a bam file of this size on your end, without me sending you one that big ? Also, the error is different after I put the scamBamParam in the right spot :
>
> Error in .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) :
> negative length vectors are not allowed
>
> Integer overflow somewhere, maybe ?
>
> - Dario.
>
> ---- Original message ----
> >Date: Sun, 12 Dec 2010 20:59:23 -0800
> >From: Martin Morgan <mtmorgan at fhcrc.org>
> >Subject: Re: [Bioc-sig-seq] scanBam Error
> >To: D.Strbenac at garvan.org.au
> >Cc: bioc-sig-sequencing at r-project.org
> >
> >On 12/12/2010 08:00 PM, Dario Strbenac wrote:
> >> Hello,
> >>
> >
> >> I'm having trouble reading in a BAM file when "seq" is one of the
> >strings passed to the what argument of ScanBamParam. If it's not, then
> >the the reading completes successfully. I don't understand what the
> >error means. It is :
> >>
> >> Error in .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param) :
> >> INTEGER() can only be applied to a 'integer', not a 'closure'
> >>
> >> The traceback is :
> >>
> >>> traceback()
> >> 4: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...)
> >> 3: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param)
> >> 2: scanBam("HS1808.bam", flag = ScanBamFlag(isDuplicate = FALSE),
> >> param = ScanBamParam(reverseComplement = TRUE, what = c("rname",
> >> "strand", "pos", "seq")))
> >> 1: scanBam("HS1808.bam", flag = ScanBamFlag(isDuplicate = FALSE),
> >> param = ScanBamParam(reverseComplement = TRUE, what = c("rname",
> >> "strand", "pos", "seq")))
> >>
> >> and the environment is :
> >>
> >> R version 2.12.0 (2010-10-15)
> >> Platform: x86_64-pc-mingw32/x64 (64-bit)
> >>
> >> locale:
> >> [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C LC_TIME=English_Australia.1252
> >>
> >> attached base packages:
> >> [1] stats graphics grDevices utils datasets methods base
> >>
> >> other attached packages:
> >> [1] Rsamtools_1.2.1 Biostrings_2.18.0 GenomicRanges_1.2.0 IRanges_1.8.2
> >>
> >> loaded via a namespace (and not attached):
> >> [1] Biobase_2.8.0
> >
> >Hi Dario -- this is some kind of error in Rsamtools' C code, but I'm not
> >able to reproduce it on my end so can't track it down. Is there any way
> >of producing and sharing with me an example file that has this problem?
> >
> >One thing (not causing the bug) in your traceback is that 'flag' should
> >be an argument to ScanBamParam; as it is I think it is being silently
> >ignored.
> >
> >Martin
> >
> >>
> >> --------------------------------------
> >> Dario Strbenac
> >> Research Assistant
> >> Cancer Epigenetics
> >> Garvan Institute of Medical Research
> >> Darlinghurst NSW 2010
> >> Australia
> >>
> >> _______________________________________________
> >> Bioc-sig-sequencing mailing list
> >> Bioc-sig-sequencing at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >
> >
> >--
> >Computational Biology
> >Fred Hutchinson Cancer Research Center
> >1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> >
> >Location: M1-B861
> >Telephone: 206 667-2793
>
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--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
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