[Bioc-sig-seq] PDict question

[Raphael Gottardo]

You need to use a 64 bit version of R.

Raphael

On 3-Jun-08, at 8:21 AM, Joseph Dhahbi, P.h.D. wrote:

> Hello
> I need help on how to get around the memory error reported below,  
> especially when I can not add anymore RAM:
> Here is the Hardware Overview:
>  Model Name:	Mac Pro
>  Model Identifier:	MacPro1,1
>  Processor Name:	Dual-Core Intel Xeon
>  Processor Speed:	2.66 GHz
>  Number Of Processors:	2
>  Total Number Of Cores:	4
>  L2 Cache (per processor):	4 MB
>  Memory:	20 GB
>  Bus Speed:	1.33 GHz
>  Boot ROM Version:	MP11.005C.B08
>  SMC Version:	1.7f10
>  Serial Number:	G87052SGUPZ
>
>
>
>> NM_seq=readSolexaFastA(NM_fa)
>> NM_alf=alphabetFrequency(NM_seq, baseOnly=TRUE)
>> NM_seq_clean = NM_seq[NM_alf[,"other"]==0]
>> length(NM_seq)
> [1] 4820218
>> length(NM_seq_clean)
> [1] 4817537
>> NM_seq_clean
>  A DNAStringSet instance of length 4817537
>          width seq
>      [1]    36 GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGGAT
>      [2]    36 GTGGTAATTCATCAGATCTCGGATGGCATTGGTCAT
>      [3]    36 GGGAGGTCACTAATGGAGACACACAGAAATGTAACA
>      [4]    36 GGGATTGGTTTTTTGTTACTGATTTGTTTGAGTTCA
>      [5]    36 GTGGTAATTTTGACTTTTTAGGTTAATTTATTTTTT
>      [6]    36 GATCGGAAGGAGCTCGTATGCCGTCTTCTGCTTAGA
>      [7]    36 GGTCAGTTGTGTTCTCCTGAGTAGGTTGTGTGAATG
>      [8]    36 GGGAGGTCACTAATGGAGACACACAGAAATGTAACA
>      [9]    36 GGGAGGCTGAGGCAGGAGAATGGCATGAACCTAGAT
>      ...   ... ...
> [4817529]    36 TTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAG
> [4817530]    36 CATCAATGTATCTTAAGGCGTAAATTGTAAGCGTTA
> [4817531]    36 CGAGCAGCGACGCATCACCCAGCTAGATCGGAAGAG
> [4817532]    36 GCAATGCCACTGGCGCGACAACCGGGACACCATAGG
> [4817533]    36 CCTCGCCGGACACGCTGAACTTGTGGCCGTTTTCGT
> [4817534]    36 CCATTGTACAACGTATCGACATATCCTCCACCCGCC
> [4817535]    36 CCCCCTGAACCTGAAACATAAAATGAATGCAATTGT
> [4817536]    36 ACCATGTTGTCCAAGGGCGAATTCTGCAGATATCCA
> [4817537]    36 CAGGGGCCGGCGGCTGGCTAGGGCTGCAGCGTTAAA
>
>> NM_seq_pDict=PDict(NM_seq_clean)
> Error in .PDict(dict, names(dict), tb.start, tb.end, drop.head,  
> drop.tail,  :
>  alloc_actree_nodes_buf(): failed to alloc actree_nodes_buf
> R(433,0xa000d000) malloc: *** vm_allocate(size=4032987136) failed  
> (error code=3)
> R(433,0xa000d000) malloc: *** error: can't allocate region
> R(433,0xa000d000) malloc: *** set a breakpoint in szone_error to debug
>
>> sessionInfo()
> R version 2.7.0 (2008-04-22)
> i386-apple-darwin8.10.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils    datasets   
> methods   base
>
> other attached packages:
> [1] BiostringsCinterfaceDemo_0.1.2 Biostrings_2.8.9               
> Biobase_2.0.1
>
>
>
>
> Regards,
> Joseph
>
> Joseph M. Dhahbi, PhD
> Childrens Hospital Oakland Research Institute
> 5700 Martin Luther King Jr. Way
> Oakland, CA 94609
> USA
> Ph.(510)428-3885 EXT.5743
> Cell.(702)335-0795
> Fax (510)450-7910
> jdhahbi at chori.org
> The email message (and any attachments) is for the sol...{{dropped:26}}