Re: [MUMmer-help] delta-filter memory usage

[Adam P. <aph...@gm...>]

Hi Greg,
It is possible that the loaded delta file could consume more memory than
the original file. The file format is different than the data structure
that is built from that file. 9GB is also quite large for a delta file, and
usually an signal to use more conservative alignment parameters, e.g. a
larger seed size, the -mumreference option, larger cluster size, etc.

Best,
-Adam


On Tue, Jul 14, 2015 at 2:03 PM, G. Magoon <gre...@gm...> wrote:

> Hi,
> I have a ~9 GB .delta file that I'm trying to filter with delta-filter
> (MUMmer 3.23) on a computer with 16 GB RAM (+ 4 GB swap space). Within a
> minute or two of launching, the delta-filter process takes up essentially
> the entire system memory and is eventually killed by the system, apparently
> without having produced any output. I'm new to MUMmer, but my naive
> expectation was that it would only need enough memory to store the full
> delta file (at most).
>
> Is this high memory usage expected? If so, is there a way to estimate the
> memory that would be required for the delta-filter process to complete
> successfully?
>
> Thanks very much in advance,
> Greg
>
>
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