From: Bernd J. <ber...@pa...> - 2009-04-27 14:42:08
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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 |