[mira_talk] Re: MIRA disk space issue
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 15 Apr 2011 23:55:54 +0200
On Friday 15 April 2011 23:44:07 Robert Bruccoleri wrote:
> What's new in 3.2.1.13?
The "CHANGES.txt" is your friend there :-)
Depending on which version he used (I'd guess 3.2.1), the following fixes will
apply when it comes to disk/memory usage:
directly after 3.2.1:
- for mapping Solexa data, MIRA now reduces unnecessary mapping attempts when
no more reads match a contig. This should save a bit of time, especially in
projects with lots (>1000) of reference sequences.
(3.2.1.2)
- assembly of millions of EST/RNASeq now *way* faster. E.g.: 10m Solexa reads
(100bp) down from several days to ~1 day.
(3.2.1.4)
- improved internal handling of invalid overlaps. Effectively slashes memory
needed there by a factor of 8 to 10. E.g.: in Solexa transcriptome 10m reads
@ 100bp with quite some ploidy, uses just ~1 GiB instead of ~11.5 GiB
(3.2.1.7)
- fixed memory allocation bug which led MIRA to perform a couple of more
allocations than necessary.
- new routines to choose and trim down SKIM hits. Save tremendous amount of
disk and memory for high coverage projects (coverages >50x), especially when
coverages reach >100x.
(3.2.1.9)
- SKIM now uses intermediate result purging, tremendously reducing size of
result files in large assemblies.
- bugfix: SKIM sometimes saved wrong hits when there were effectively none
- bugfix: large increases of virtual memory needs between the passes have been
cut down.
(3.2.1.11)
- bugfix for regression in 3.2.1.10: in mapping mode, SKIM made too many
comparisons, in the order of a de-novo assembly
(3.2.1.13)
- more efficient disk I/O for hash statistics analysis
B.
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