[mira_talk] Re: Make us check a part of results
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 15 Jun 2009 23:35:08 +0200
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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