From: Nava W. <ne...@sg...> - 2009-04-27 14:30:00
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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 |