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@uq.edu.au Web: http://www.di.uq.edu.au -----Original Message----- From: Dario Strbenac Reply-to: D.Strbenac@garvan.org.au To: bioc-sig-sequencing@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 >Subject: Re: [Bioc-sig-seq] scanBam Error >To: D.Strbenac@garvan.org.au >Cc: bioc-sig-sequencing@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@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 _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing [[alternative HTML version deleted]]