[Bioc-sig-seq] Slow/hanged QA on Illumina Data

[Ivan Gregoretti]

It sounds like you may have run out of memory in your linux box.

When I run qa() in my 16GB machine, it usually uses ~14GB just for
this qa() process.

That is for 36 bases. May be, it you are running 75 bases, you just
used all the RAM.

Is the processor running 100%? Check it issuing 'top' at the command
line. If it is, then you are good.

'top' can also tell you is you are swapping wildly. (swapping is when
your machine runs out of RAM memory and starts storing data in a
temporary location in you hard drive to avoid crashing.)

Ivan


Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1592
Fax: 1-301-496-9878

> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-08-12 r49169)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base







On Thu, Sep 10, 2009 at 4:35 PM, Pratap, Abhishek
<APratap at som.umaryland.edu> wrote:
> Hi  Martin
>
>
>
> I am noticing a lethargic or may be hanged processing with qa()
> function in ShortRead. I know I have raised this question before.
> Recently I have updated my R to dev version and installed latest
> bioconductor.Currently I am trying to run qa()  on 8 lanes of data for
> 75 bp reads.  The CPU is 16 cores with 16 GB RAM.
>
>
>
> It has been two hours since the processing has been going on. Is it
> usually takes so long. I am not sure.  Will using Rmpi help ?
>
>
>
>
>
> Thanks,
>
> -Abhi
>
>
>
> sessionInfo()
>
> R version 2.9.2 (2009-08-24)
>
> x86_64-unknown-linux-gnu
>
>
>
> locale:
>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
> TF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=
> C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATI
> ON=C
>
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
>
>
> other attached packages:
>
> [1] ShortRead_1.2.1   lattice_0.17-25   BSgenome_1.12.3
> Biostrings_2.12.8
>
> [5] IRanges_1.2.3
>
>
>
> loaded via a namespace (and not attached):
>
> [1] Biobase_2.4.1 grid_2.9.2    hwriter_1.1
>
>
>
>
>
>
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>
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