[Bioc-sig-seq] readAligned error

[kirti prakash]

Hi Steve,

First of all I would like to thank you as I was able to plot tag
densities for a couple of histone modifications.

I have 6 .map files from bowtie for 6 histone modifications. So for
first couple of files it read fine but then it gave me this error...

I already had 2 readaligned data stored in my system when I read the
3rd file. I removed the objects by rm(me3) and tried again but again
it gave me the error.

I also think its the problem of ram but is it possible to have all the
objects in memory as they would be needed during plotting.

Thank you,

Best regards,

Kirti Prakash

On Mon, Aug 30, 2010 at 8:01 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi,
>
> On Mon, Aug 30, 2010 at 12:48 PM, kirti prakash
> <kirtiprakash3.14 at gmail.com> wrote:
>> Hi,
>>
>> I am getting this error...
>>
>> me3 <- readAligned("dirpath", type="Bowtie")
>> Error: Input/Output
>>  'readAligned' failed to parse files
>>  dirPath: 'xxx'
>>  pattern: ''
>>  type: 'Bowtie'
>>  error: Calloc could not allocate (9638489 of 4) memory
>>
>> I have some six histone modifications files... I didn't got this error
>> for the first couple of files that I read.
>
> What do you mean "with the first couple of files you read"?
>
> Did you execute this command before in a different directory or something?
>
> Do you already have some "readAligned" data sets loaded into your workspace?
>
> Is it possible that your machine is simply running out of RAM?
>
> -steve
>
>>
>> I read this thread which discussed this problem but I could not follow much...
>>
>> http://tolstoy.newcastle.edu.au/R/devel/06/01/3641.html
>>
>>> sessionInfo()
>> R version 2.11.1 (2010-05-31)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>>  [5] LC_MONETARY=C                  LC_MESSAGES=en_US.iso885915
>>  [7] LC_PAPER=en_US.iso885915       LC_NAME=C
>>  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] grid      stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] HilbertVis_1.6.0    ShortRead_1.6.2     Rsamtools_1.0.7
>> [4] lattice_0.18-8      Biostrings_2.16.9   GenomicRanges_1.0.7
>> [7] IRanges_1.6.13      biomaRt_2.4.0
>>
>> loaded via a namespace (and not attached):
>> [1] Biobase_2.8.0 hwriter_1.2   RCurl_1.4-3   tools_2.11.1  XML_3.1-0
>>
>> Best regards,
>>
>> Kirti Prakash
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>