[mira_talk] Re: Error / bug report filed as Ticket #82
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 14 May 2012 13:15:28 +0200
On May 13, 2012, at 19:49 , David Laehnemann wrote:
> just filed a Ticket and as requested, I give a short notification over the
> list. It seems MIRA decided to stop the de novo assembly of Illumina
> paired-end reads due to an "Internal logic/programming/debugging error". And
> even from looking in the log-file, I don't understand what that means or what
> caused it...
>
> Well, all the details should be in the attached log-file. If there is more
> info needed, please just contact me via eMail.
Seen it.
The primary cause for the trouble is that you are using way too much data. A
first estimation of MIRA would be that you would end up with something like
400x coverage, which is a bit insane. While MIRA is not strictly an OLC
assembler, it certainly is not a de-Bruijn, and then the amount of overlaps
gets important.
Try doing an assembly with, say, 4 to 5m reads, that will work quite nicely and
you will still have more than enough data & coverage.
B.
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