[BioC] Error: cannot allocate vector of size 649.8 Mb

[Martin Morgan]

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 at 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