Re: [Swiftng-users] long run times

[Nava W. <ne...@sg...>]

How big is dm3_ucsc.fa? Swifts aligner is very slow and only designed to
deal with 5000bp sequences.

Are you saying it took 39 hours using the parameters settings in the
svn? That would be a bit odd, if you can send me the stdout/err that
would be useful.

Sorry, for the delay in getting back to you on your xml questions. I've
not forgotten! Just snowed under.

Nav

On Mon, Apr 27, 2009 at 04:07:06PM +0200, Bernd Jagla wrote:
> Nava,
> 
>  
> 
> Here is a list of parameters I tested and associated run-times (143,343.85
> sec = 39hrs!!!!) for one tile.
> 
> Could you please comment on where all the time might be spent?
> 
>  
> 
> I would like to understand the problem to be able to optimize our protocols.
> 
>  
> 
> It doesn't really seem to be possible to reduce the time without loosing too
> many clusters.
> 
>  
> 
> Thanks,
> 
>  
> 
> Bernd
> 
>  
> 
> Time  = [sec] user time from time command
> 
> Wc pf = number of lines in *.pf files
> 
> Wc nonpf =  numbe of lines in *.nonpf files
> 
> There is only one parameter changed compared to the standard (normal) call
> of the program. 
> 
>  
> 
> idx   parameter  time  wc pf wc nonpf
> 
> 1     normal     143,343.85 182,256    1,720,580
> 
> 2     --ref dm3_ucsc.fa      27,681.68  110,988    1,809,448
> 
> 3     --correlation_cc_subimage_multiplier 20  114,063.20 179,724
> 1,695,836
> 
> 4     --correlation_cc_subimage_multiplier 10  34,372.92  154,840
> 1,751,684
> 
> 5     --correlation_cc_subimage_multiplier 40  4,732.95   116,920
> 1,801,616
> 
> 6     --threshold_window 3   2,311.50   131,260    664,312
> 
> 7     --threshold_window 4   2,226.00   106,416    261,468
> 
> 8     --segment_cycles 2     3,343.96   143,712    1,301,216
> 
> 9     --segment_cycles 1     2,266.62   142,016    772,496
> 

-- 
Nav

Work: 01865 854873
Mob : 07518-358405