Note that you are probably not using a 64bit version of R, so you
cannot utilize all of your 8MB. Check by looking at .Machine
$sizeof.pointer
As a minimum upgrade to R-2.9, if you want to use bioconductor for
short reads.
Kasper
On Jun 24, 2009, at 11:37 , Anastasia Gioti wrote:
Dear list,
I just started playing with shortReads package in order to read
fastaq files from the illumina analyzer, and i have some issues.
The most important is the fact that the readFastaq crashes because
of memory I suppose when i try to read files >1GB. Ex:
fqpattern='s_3_1_sequence.txt'
> afrN=file.path(analysisPath(sp), fqpattern)
> afrN
[1] "/Users/nat/Data/Illumina/Solexa_disk_modforR/Data/
HJSN_FC1_280409_3//Data/C1-C55Firecrest/
Bustard1.3.2_06-05-2009_rdixon/GERALD_06-05-2009_rdixon/
s_3_1_sequence.txt"
> afrNq=readFastq(sp, fqpattern)
Error: cannot allocate vector of size 27.0 Mb
R(1337,0xa07a2720) malloc: *** mmap(size=28340224) failed (error
code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
R(1337,0xa07a2720) malloc: *** mmap(size=28340224) failed (error
code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
I only succeeded in reading a file < 1GB, but i suppose that the
shortReads class is designed for big files ;-).
Another minor issue is the names of the folders in the Illumina
output directory that I need to designate in exptPath so that
p=SolexaPath(exptPath) is correctly parsed. I finally managed to
find the logic behind this, but I would like to confirm that the
path absolutely needs to contain this string: Data/C1-
C(readlength)Firecrest. At least in my hands it would not work with
other names (which are currently produced by illumina, for ex IPAR
instead of Firecrest). Is that correct? Maybe this parser is hard
coded for previous versions of Illumina outputs? In that case is
there any plan to update it? Although this is not very important
I use R2.8 on a Leopard with 8GB of memory, so I think that my
problem with fastq does not come from my computer...
Any help /suggestions are welcome!
Thank you,
Anastasia Gioti
Post-Doc, Evolutionary Biology Department
Upssala University
Norbyvagen 18D
SE-752 36 UPPSALA
[email protected]
Tel: +46-18-471 6465
Fax: +46-18-471 6310
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