[mira_talk] Re: empty results folder
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 21 Feb 2009 11:44:05 +0100
On Friday 20 February 2009 Rex Malmstrom wrote:
> I am trying to get MIRA up and running, but I'm have some difficulty.
> After running a de novo assembly of 454 FLX data, I have an empty
> *_results directory. The *_info_assembly.txt was created and
> indicates the sequences were assembled and contigs were formed, but
> there are no files in the _results directory. Any ideas? Thanks.
Hi Rex,
I've taken a peek at the log file and the directory listing: MIRA stopped in
the midst of the fourth pass and did not finish correctly. As the STDERR output
was not redirected to the log file, I can only speculate on the reason.
Assuming that it was not a simple CTRL-C or other kill, the only plausible
thing I can think of is that you are running the 32 bit version and that you
encountered an out of memory error along the way. The reason why I think that
this is the case is because you've got some really high coverage (~180x),
which is good per se but becomes a problem as one of the tables grows to sizes
(2.5 GiB) that is dangerous for a 32 bit machine.
There are several possibilities to remedy the problem and tell MIRA to use
less memory. The best one being a version with some new algorithms that take
care not to lead to an explosion of memory usage. But I'll contact you by mail
for that.
Regards,
Bastien
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