Yes, i already checked the permissions

$ ls -l s6_plantula.fq
-rwxrwxrwx 1 marco marco 2618477626 2010-08-11 18:38 s6_plantula.fq

any other idea?


On Fri, Aug 20, 2010 at 1:45 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 08/20/2010 11:22 AM, Marco Ortiz wrote:
> > Hi
> >
> > Thanks to respond. I checked and the file path is correctly because i
> could
> > open a similar file but about 38 Mb, that's why i  thought that the
> memory
> > was the problem, here is:
> >
> >
> >
> >> control <- readFastq("ControlB_2A8_130_50.250k.fq",
> > qualityType="SFastqQuality")
> >> seedling <- readFastq("s6_plantula.fq", qualityType="SFastqQuality")
> > Error en .local(dirPath, pattern, ...) : cannot open file s6_plantula.fq
>
> From the shell, do you have read permissions for this file?
>
>  % ls -l s6_plantula.fq
>
> Martin
>
> >> control
> > class: ShortReadQ
> > length: 250000 reads; width: 36 cycles
> >
> >
> >
> >
> > Here the sessionInfo(), but i'm not sure that it has to give me the info
> > about the hardware andf software
> >
> >
> >
> >> sessionInfo()
> > R version 2.10.1 (2009-12-14)
> > i486-pc-linux-gnu
> >
> > locale:
> >  [1] LC_CTYPE=es_MX.utf8       LC_NUMERIC=C
> >  [3] LC_TIME=es_MX.utf8        LC_COLLATE=es_MX.utf8
> >  [5] LC_MONETARY=C             LC_MESSAGES=es_MX.utf8
> >  [7] LC_PAPER=es_MX.utf8       LC_NAME=C
> >  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=es_MX.utf8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] ShortRead_1.4.0    lattice_0.18-3     BSgenome_1.14.2
> >  Biostrings_2.14.12
> > [5] IRanges_1.4.16
> >
> > loaded via a namespace (and not attached):
> > [1] Biobase_2.6.1 grid_2.10.1   hwriter_1.2
> >
> >
> >
> >
> >
> >
> >
> > On Fri, Aug 20, 2010 at 11:23 AM, Martin Morgan <mtmorgan@fhcrc.org>
> wrote:
> >
> >> On 08/20/2010 08:19 AM, Marco Ortiz wrote:
> >>> * Hi All, ** ** I am new to the world of R and Bioconductor and I had
> >>> the** following error when I try to read a fastaq file of 2 Gb****
> >>> First I try to run it in Linux, but there i had an error that tell me
> >>> *
> >>>
> >>> * <**
> >>>
> >>> Error: (dirPath, pattern, ...) cannot open file
> >>>
> >>> *
> >>>
> >>> * Then i try to run it in Windows and there i had this error*
> >>>
> >>> *
> >>> *
> >>>
> >>> *
> >>> *
> >>>
> >>> * > library(ShortRead)*
> >>>
> >>> *** > plantula <- readFastq("s6_plantula.fq",
> >> qualityType="SFastqQuality")*
> >>>
> >>> *** Error: cannot allocate vector of size 649.8 Mb*
> >>
> >> This is likely limited memory problem; R is saying 'I allocated some
> >> memory, and now I'm trying to allocate 649.8Mb more, and that additional
> >> memory allocation fails'. Memory limits on 32-bit windows systems are
> >> hard to get around; you're better using a 64-bit Windows or Linux
> >> system. Your Linux problem seems really  straight-forward -- you haven't
> >> specified the file path correctly. Your R likely has command completion,
> so
> >>
> >>  readFastq("~/
> >>
> >> and then use the tab key to complete the path.
> >>
> >> Please include sessionInfo() when you're posting to the list; it makes
> >> clear what software and hardware you're using.
> >>
> >> Martin
> >>>
> >>> *
> >>> *
> >>>
> >>> * *
> >>>
> >>> * Then i **set memory.size() at 3000 as well as memory.limit() but i'm
> >>> already having the problem*
> >>>
> >>> * i has a processor of 32 bits, a virtual memory of 3754 Mb*
> >>>
> >>> *  ** Can someone tell me if this is due to an improper configuration,
> >>> lack** of sufficient memory, etc?*
> >>>
> >>>
> >>
> >>
> >> --
> >> 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
> >>
> >
> >
> >
>
>
> --
> 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
>



-- 
Marco Ortiz
Sexta generacion
Licenciatura en Ciencias Genómicas

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