Re: [Swiftng-users] long run times

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

Though it says it's not using the reference, it maybe processing a large
number of smaller contigs. I've corrected this in the latest checkin of
swift but it would be worth trying this tile with no reference
specified.

Other than that, it does look like the tile is generating an abnormally
large number of clusters. If possible can you send me a sample tile?

On Mon, Apr 27, 2009 at 04:41:51PM +0200, Bernd Jagla wrote:
> Here are the associated output-files...
> The one with the worst times unfortunately hasn't gotten any stdout/err for
> some odd reason. Here is second "best"...
> 
> 
> -----Original Message-----
> From: Nava Whiteford [mailto:ne...@sg...] 
> Sent: Monday, April 27, 2009 4:30 PM
> To: Bernd Jagla
> Cc: 'Tom Skelly'; Swi...@li...
> Subject: Re: long run times
> 
> How big is dm3_ucsc.fa? Swifts aligner is very slow and only designed to
> deal with 5000bp sequences.
> 
> ->Dm3 is not being used (too big)...
> 
> 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.
> 
> ->See attached
> 
> Sorry, for the delay in getting back to you on your xml questions. I've
> not forgotten! Just snowed under.
> 
> ->no worries... it is cold here in Paris too today, but not that cold ;)...
> Good luck !!
> 
> 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



-- 
Nav

Work: 01865 854873
Mob : 07518-358405