[mira_talk] Re: Make us check a part of results

On Montag 15 Juni 2009 Kenta SHIRASAWA wrote:
> 1)
>    We will use a mira_out.txt output for a further analysis. We are
> happy if MIRA makes a result txt file one by one contig, or adds a
> created contig to a result txt file, because we can check a part of
> results without waiting for finishing whole assemblings.

Well, MIRA has no other possibility ... to save memory, contig structures get 
freed and re-allocated once a contig has been finnished. The update of the 
files 
on the fly is merely a (very welcome) side effect :-)

> 2)
>    Can you estimate how long time does MIRA take for finishing an
> assemble 500,000 454-reads (ca. 200 Mb) with the options "-fasta
> -job=denovo,est,draft,454 -notraceinfo -SB:lsd=yes -SK:pr=95 -SK:mnr=yes
> -OUT:ort=yes"?
>    Our machine (64bit linux, 2 GHz CPU, 128 GB memory) has been running
> for more than a week.

Something's wrong there, plain wrong. May I ask you to send me the output log 
of the assembly to have a look at?

> 3)
>    Please tell us a difference between conting headers, e.g., mira_c#
> and mira_lrc#.

I really need to document that: it's a remainder of larger changes that are 
currently made in the algorithms, it was introduced more for debugging 
purposes but a few users thought it could help them so I left it in.

Basically, MIRA starts to build contigs in areas that are "rock solid", i.e., 
not a repetitive region (main decision point) and nice coverage of good reads. 
If during the assembly MIRA reaches a point where it cannot start building a 
contig in a non-repetitive region, it will name the contig "lrc" instead of 
"c".

Of course, this naming convention is a bit weird (not to say: useless) when 
having to assemble ESTs, but at the moment I didn't build in code that 
switches of contig naming in these cases.


Regards,
  Bastien


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