Hi All, I have tried to use import.gff3 from the rtracklayer package to import annotation information for the mosquito genome (gff3 file here: http://aaegypti.vectorbase.org/GetData/Downloads/) which is only 20 MB but the memory usage has exceeded 100GB on one of our high memory servers. This seems like far too much to just read in the file (which takes only 3 seconds with read.delim) and convert to RangedData objects. Has anyone experienced similar problems? Here is my sessionInfo: R version 2.13.0 (2011-04-13) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.8.0 rtracklayer_1.12.4 RCurl_1.5-0 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biostrings_2.20.0 BSgenome_1.20.0 GenomicRanges_1.4.1 [4] IRanges_1.10.0 tools_2.13.0 XML_3.2-0 -- Vince Buffalo Statistical Programmer Bioinformatics Core UC Davis Genome Center University of California, Davis "There's real poetry in the real world. Science is the poetry of reality." -Richard Dawkins [[alternative HTML version deleted]]

Are you sure this is valid GFF3? For example, consider this attribute field: ID=supercont1.1;molecule_type=dsDNA;GenBank:supercontig:AaegL1:superco nt1.1:1:5856339:1;translation_table=1;topology=linear;localization=chr omosomal; The string "GenBank:supercontig:AaegL1:supercont1.1:1:5856339:1" is delimited by semi-colons, but it does not conform to the key=value format. I will add a check for this to devel, so that the error is more obvious. You can still read this file if you use the "colnames" argument. If colnames=character(), you will get just the seqnames, start and end. If you just want the strand in addition to that, specify colnames="strand", etc. By default, all columns (including attributes) are parsed. Michael On Fri, Jul 1, 2011 at 11:48 AM, Vince S. Buffalo <vsbuffalo@gmail.com>wrote: > Hi All, > > I have tried to use import.gff3 from the rtracklayer package to import > annotation information for the mosquito genome (gff3 file here: > http://aaegypti.vectorbase.org/GetData/Downloads/) which is only 20 MB but > the memory usage has exceeded 100GB on one of our high memory servers. This > seems like far too much to just read in the file (which takes only 3 > seconds > with read.delim) and convert to RangedData objects. Has anyone experienced > similar problems? > > Here is my sessionInfo: > R version 2.13.0 (2011-04-13) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.8.0 rtracklayer_1.12.4 RCurl_1.5-0 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biostrings_2.20.0 BSgenome_1.20.0 GenomicRanges_1.4.1 > [4] IRanges_1.10.0 tools_2.13.0 XML_3.2-0 > > -- > Vince Buffalo > Statistical Programmer > Bioinformatics Core > UC Davis Genome Center > University of California, Davis > > "There's real poetry in the real world. Science is the poetry of reality." > -Richard Dawkins > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]