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

[Martin Morgan]

On 08/20/2010 12:12 PM, Marco Ortiz wrote:
> 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?

I doubt it's a memory problem. Do both of these work in R

  readLines("s6_plantula.fq", 10)
  readLines(gzcon(file("s_6_plantula.fq")), 10)

The permissions are weird (I would have guessed -rw-r--r-- or something)
but I doubt this is a problem. I guess this is supposed to be a plain
text file; is it? e.g.,

  head s6_plantula.fq

giving something reasonable. Is it mounted on an unusual file system,
e.g., can you read another file from the same location? What about just
a small fraction of this file, e.g.,

  head -n 1024 s6_plantula.fq > some_file.fq

Also not likely to be a problem, but updating to a current R / ShortRead.

Martin

> 
> 
> On Fri, Aug 20, 2010 at 1:45 PM, Martin Morgan <mtmorgan at 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 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
>>
> 
> 
> 


-- 
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