On 11/09/2010 06:52 AM, Christoph Bartenhagen wrote: > Hi again, > > thank you very much for your reply. It sounds very reasonable to me and > it explains why it works with smaller BAM-files, i.e. files containing > fewer reads. > To track down the error, here's my sessionInfo() some more info about my > error (I am not sure though how to generate a (small) reproducible > example, since the problem seems to be related to quite large alignment > files): ok thanks for the additional info. In the mean time, a workaround is to use the 'param' argument of scanBam to process smaller chunks (e.g., chromosomes) of your data at one time. Martin > >> bam = scanBam(file="alignment.bam") > Error in .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) : > negative length vectors are not allowed > >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Rsamtools_1.2.0 Biostrings_2.18.0 GenomicRanges_1.2.0 > [4] IRanges_1.8.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 > > > My BAM-file contains 69.654.881 reads of length 36bp each. > If this problem has already been adressed, do I need to update my > version of Rsamtools (1.2.0)? I just saw that the release version is > 1.2.1 and the development version is 1.3.4. > > Thanks for any further advice, > Christoph > > > Am 09.11.2010 14:52, schrieb Martin Morgan: >> On 11/09/2010 05:22 AM, Christoph Bartenhagen wrote: >> >>> Hello everyone, >>> >>> I am experiencing a strange error, while reading (large) BAM-files (> >>> 2GB) in R with the function scanBam() in the Rsamtools package. >>> It stops saying "negative length vectors are not allowed". >>> >>> I think my BAM-file is ok, because I can read it in small chunks like >>> reads on positive strand first, then reads on the negative strand (using >>> ScanBamParam). This might be a more general Error in R because it seems >>> to occur in very different R programs. >>> >>> Has anyone experienced this error? >>> I would really appreciate any ideas how to fix this problem or >>> concerning the reason for this error (I don't really understand what a >>> "negative length vector" is). >>> >> Hi Christoph -- >> >> This is an integer overflow when the (accumulated) underlying DNA or >> quality strings are too long. But I think this has been addressed and so >> your sessionInfo() and a reproducible example (or at least the explicit >> command that triggers the problem) would help. >> >> Martin >> >> >>> Thanks in advance >>> Christoph >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793