[mira_talk] Re: repeat clusters
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 9 Jun 2010 20:12:06 +0200
On Mittwoch 09 Juni 2010 bio5yz wrote:
> Thanks very much for your explanation Bastian!
> My main issue now is that I cannot find any *nasty* files in my MIRA
> directories for any of my 3 trial runs made. There are no files containing
> *nasty* anything in the *_log directories. I guess these are the files that
> i really need to determine the location, stretches, members of the masked
> repeats. Would it be possible to generate this log after MIRA has run to
> completion. Do I need to turn on a specific verbose param for it to print?
> Again my log file is saying "Mask nasty repeats (mnr) :
> no" although it does seem to be masking the repeat regions. Should I be
> turning this on manually?
Yay, today seems to be bug reporting day. Find one, get one free. Or two. Or
three.
Ok, the bug is: nasty sequences are always masked, but reported only if
-SK:mnr
is turned on.
So, for you it means: rerun with -SK:mnr=on to get the file report.
I'm sorry for the inconvenience.
Bastien
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