From: Tom S. <ts...@sa...> - 2009-04-27 14:27:36
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Ouch! If you go to the run output file (the log, not the xml) and grep out 'Memstats' lines, that will give you the start/stop and delta times of the various processing steps steps. Note that the start/stops are nested, so you need to match up a start and a stop with the same label. That should tell us where to look further. --TS 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 > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |