HI, I am trying to use ShortRead to get QCs on my bam files ( aligned with BWA) this is what I used to read my aligned files > read_bam<-readAligned(".",pattern="bam",type="BAM") then I have this error: Error: Input/Output 'readAligned' failed to parse files dirPath: '.' pattern: 'bam' type: 'BAM' error: negative length vectors are not allowedshortread I saw on a previous bioconductor mailing list that Martin Morgan gave some previous clues about this kind of error and advised to check the Bam using these commands #### Martin Morgan <http: search.gmane.org="" ?author="Martin+Morgan&amp;sort=date"> | 8 Oct 18:59 Favicon Re: Illumina QC using ShortRead Can you (a) try to read the bam file directly using param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, what = ShortRead:::.readAligned_bamWhat()) res = scanBam('./100927_s_1.bam', param=param) I think this will fail, and then traceback() #### If I do this, I get this kind output : > param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, what = ShortRead:::.readAligned_bamWhat()) > res = scanBam('./6160_7#16.bam', param=param) Error in .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) : negative length vectors are not allowed > traceback() 4: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) 3: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param) 2: scanBam("./6160_7#16.bam", param = param) 1: scanBam("./6160_7#16.bam", param = param) Could somebody advise on the best way to go forward?My Bams don't seem to be right for ShortRead, Do I need to realign my reads? Many thanks Nathalie > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=C [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.6.2 Rsamtools_1.0.8 lattice_0.18-8 [4] Biostrings_2.16.6 GenomicRanges_1.0.4 IRanges_1.6.13 loaded via a namespace (and not attached): [1] Biobase_2.8.0 grid_2.11.1 hwriter_1.3 tools_2.11.1 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

Hi Nathalie I think your bam files are too large for your version of R! I suggest using the development version of R then biocLite('ShortRead') then trying again. Martin -- Martin Morgan On Aug 19, 2011, at 16:47, Nathalie Conte <nac at="" sanger.ac.uk=""> wrote: > HI, > > I am trying to use ShortRead to get QCs on my bam files ( aligned with BWA) > this is what I used to read my aligned files > > read_bam<-readAligned(".",pattern="bam",type="BAM") > then I have this error: > Error: Input/Output > 'readAligned' failed to parse files > dirPath: '.' > pattern: 'bam' > type: 'BAM' > error: negative length vectors are not allowedshortread > I saw on a previous bioconductor mailing list that Martin Morgan gave some previous clues about this kind of error and advised to check the Bam using these commands > #### Martin Morgan <http: search.gmane.org="" ?author="Martin+Morgan&amp;sort=date"> | 8 Oct 18:59 > Favicon > > > Re: Illumina QC using ShortRead > > Can you (a) try to read the > bam file directly using > > param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, > what = ShortRead:::.readAligned_bamWhat()) > > res = scanBam('./100927_s_1.bam', param=param) > > I think this will fail, and then > > traceback() > > > > #### > If I do this, I get this kind output : > >> param = ScanBamParam(simpleCigar = TRUE, reverseComplement = TRUE, > what = ShortRead:::.readAligned_bamWhat()) >> res = scanBam('./6160_7#16.bam', param=param) > Error in .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) : > negative length vectors are not allowed >> traceback() > 4: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) > 3: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param) > 2: scanBam("./6160_7#16.bam", param = param) > 1: scanBam("./6160_7#16.bam", param = param) > > > Could somebody advise on the best way to go forward?My Bams don't seem to be right for ShortRead, Do I need to realign my reads? > Many thanks > Nathalie > > > >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=C > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.6.2 Rsamtools_1.0.8 lattice_0.18-8 > [4] Biostrings_2.16.6 GenomicRanges_1.0.4 IRanges_1.6.13 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 grid_2.11.1 hwriter_1.3 tools_2.11.1 > > > > > > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. > > _______________________________________________ > 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