[mira_talk] Re: mira denovo assembly of solexa reads
- From: Saima Zubair <saim_zub@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 17 Jan 2011 05:42:33 -0800 (PST)
My expected genome size is about 2.1 to 2.2 MB. The version I am using is 3.2.0
________________________________
From: Lionel Guy <guy.lionel@xxxxxxxxx>
To: mira_talk@xxxxxxxxxxxxx
Sent: Mon, January 17, 2011 2:04:26 PM
Subject: [mira_talk] Re: mira denovo assembly of solexa reads
Hi Saima,
What's your genome size (expected)? If you get very, very high coverage, you
could have sky-high number of skims... (although 2^31 seems pretty big). What
version of mira are you using?
Cheers,
Lionel
On 17 Jan 2011, at 13:52 , Saima Zubair wrote:
> Hi,
>
> I am doing the denovo assembly of solexa reads of 100 bps long. My data is in
>the form of two mate_pair files, each file is of 3 GB. My assembly runs
>strangely for more than a week and then following error occurs with controlled
>program stop;
>
>
> Internal logic/programming/debugging error (*sigh* this should not have
>happened).
>
> "More than 2^31 skim hits would be taken ... this was not foreseen yet.
>
> ->Thrown: void Assembly::reduceSkimHits4(int32 version, const string prefix,
>const string postfix, const string logname)
> ->Caught: main
>
> Aborting process, probably due to an internal error.
>
> I have tried it with many different parameters but assembly is not complete
>yet. Should I filter the data before running command?
>
>
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