On 03/23/2010 05:00 PM, Sirisha Sunkara wrote: > Hi Martin, > > Using the ShortRead package, for files > 6.5 Gb size, I seem to be > running into this error using the readFastq function: > > Error in .Call(.read_solexa_fastq, src, withIds) : > negative length vectors are not allowed > > If this is memory related - is there a work-around to working with the > entire file?
Hi Sirisha, This is addressed in the 'devel' version of ShortRead, for which you would need to install the 'devel' version of R and then re-install Bioconductor packages. The workaround is to use an external tool (e.g., the command 'split' in linux) to split the file into smaller chunks (split files using the -l command and such that lines are multiples of 4). Martin > > Thank You, > Sirisha > >> sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-unknown-linux-gnu > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] ShortRead_1.4.0 lattice_0.17-26 BSgenome_1.14.2 > Biostrings_2.14.12 > [5] IRanges_1.4.11 > loaded via a namespace (and not attached): > [1] Biobase_2.6.1 grid_2.10.1 hwriter_1.1 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
