[mira_talk] Re: caf2gap error
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 3 Nov 2010 20:11:54 +0100
On Dienstag 02 November 2010 Brian Forde wrote:
> I recently finished a mapping assembly where I mapped 12 million illumina
> reads to my reference sequence. The CAF and ACE files produced are enormous
> (approx 7gb each).
Uh ... not good. This point to a wildly different reference sequence compared
to the bug you sequenced.
Or did you switch of the merging of Solexa reads?
> Not surprisingly when I try to convert the caf file to a
> gapdb it fails with the following error
>
> !! FATAL ERROR: system error 12 Cannot allocate memory
> !! Memory allocation failure when requesting -1701314560 bytes
> Aborted
Looks like a problem of caf2gap, indeed.
> Is there a way which I can reduce the size of the CAF file
Does your reference consist of several sequences? If yes, the it would be very
easy to split the MAF into several MAFs, convert these to CAF and these then
to single gap3 databases.
> or is there
> another genome editor I can use
gap5 could be a solution. I think James has an input filter to read SAM/BAM
(but not sure). You could use Peters script to convert MAF to SAM and then
further on to gap5.
Or you use a viewer (like Tablet), but this doesn't have an editor.
B.
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