[mira_talk] Re: Please consider
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 15 May 2013 23:22:33 +0200
On May 15, 2013, at 15:23 , monithamohan harilkumar <moniharil@xxxxxxxxx> wrote:
> Thanks for your response, But MY doubt is , it kind of generated 2 terabyte
> of tmp files, its expected to get full disk then..!!!!
> I am trying to do mapping with paired end data where each file of paired end
> is 13G and and my backbone file from oryza (reference) is 373M.The tmp
> directory created in mira are
I feel your pain.It might have been helpful for you to note how many percent
the overlap search was done when it stopped because of full disk. One could
have made a guess how much space in total would be required.
It looks like mapping of short reads to higher eukaryotes is not well optimised
in MIRA, especially if they contain lots of repeats. There is nothing you can
do except provide more disk space. In the end it might very well be that you
need to resort to other programs.
>
> -rw-r--r-- 1 monitha ctx 3736931776 May 1 01:36 mira4_int_clippings.0.txt
> -rw-r--r-- 1 monitha ctx 6882733 Apr 30 14:00
> mira4_int_clippings_t0.0.txt
If you want to recover a bit of disk space, you can delete/move away the
*clippings* files: they just contain text info on what MIRA clipped where and
why in your reads.
Sorry not to have better news,
Bastien
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