[Bioc-sig-seq] Fastq File size limit in the Short Read Package

[Martin Morgan]

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
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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