[mira_talk] Re: Internal logic/programming/debugging error
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 27 Aug 2012 20:57:01 +0200
On Aug 27, 2012, at 19:48 , John Nash wrote:
> I'm not sure if it is good news or bad news but I re-ran the job with :not=1
> and it worked perfectly.
Well, that was expected :-)
> Interesting that if you look at the project_d_info/project_assembly.txt
> reports for 3.4 vs. 3.9.1, they are very different. But I am going to pretend
> that they are not for now (because I have a very closely related genome to
> reference from) :)
The 3.9.1 version should be better. Hrmmm, I admit, I have to say that, but ...
well, most importantly, the 3.9.x series works in"fire & forget" mode: contigs
to not contain detected misassemblies anymore. In earlier version MIRA would
say in the last pass, if there were still misassemblie): "hey, look at contigs
x, y and z because there are unresolved repeat markers" (marker for
misassemblies).
Many people did not do that (unfortunately) and simply used the results as they
were *sigh*
Anyway, 3.9.x has to be better. Which means: if you have an example for the
contrary, I want the data to get that fixed :-)
B.
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