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HYPHY Package >> HyPhy bugs >> Early end to optimization in version 2.00 http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1257360746 Message started by nathanclark111 on Nov 4th, 2009 at 10:52am |
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Title: Early end to optimization in version 2.00 Post by nathanclark111 on Nov 4th, 2009 at 10:52am
I have a script that optimizes just fine in versions 0.99 and 1.00. However, in version 2.00 the optimization frequently stops prematurely at a very low likelihood value (such as -1e+100). :-?
I am running HyPhy version2.0020090803beta for MacOS(Universal Binary). I'm able to use version 1.00 as a work-around, but I thought you'd like to know in the interest of development. I've attached a .tar.gz file containing the script and data. Just run the "run_this_script" script and the analysis will start. The models "nullA" and "nullB" are run for pairs of genes. Each report line has the model name, #parameters, log likelihood, and some other parameters. NullA and nullB will not have the same max likelihood, but they will be somewhat close. Notice how some model optimizations stop very early. I've also included a SAMPLE_output file. Thanks! :) |
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Title: Re: Early end to optimization in version 2.00 Post by Sergei on Nov 4th, 2009 at 10:59am
Hi Nathan,
Thank you very much for reporting the issue. I would love to identify the problem, but I don't see an attachment with the files I need to recreate it. Could you confirm that the attachment went through, and barring that - e-mail it to me? Sergei |
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Title: Re: Early end to optimization in version 2.00 Post by nathanclark111 on Nov 4th, 2009 at 12:13pm
It didn't like the file suffix. Attaching again.
 http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=bug_report_tar.zip (27 KB | ) |
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Title: Re: Early end to optimization in version 2.00 Post by Sergei on Nov 4th, 2009 at 1:56pm
Hi Nathan,
I fixed an issue (last week), which would cause the behavior you saw. Could you please retry the script on the newest v2.0 build? I ran your example, and the -1e100 and -1e26 cases both disappeared. Cheers, Sergei |
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Title: Re: Early end to optimization in version 2.00 Post by Sergei on Nov 5th, 2009 at 2:51am
The results of running the test file using the latest (20091103) build and default OPTIMIZATION_PRECISION.
octamonkey:HYPHY sergei$ HYPHYMP 8 ~/Desktop/UserData/bug_report_091104/run_this_script.hyphy Gene List:{"0":"Nup75", "1":"Nup96", "2":"Nup98", "3":"Nup107", "4":"Nup133", "5":"Nup153"} The following comparisons will be made: 1 Nup75 Nup96 2 Nup75 Nup98 3 Nup75 Nup107 4 Nup75 Nup133 5 Nup75 Nup153 6 Nup96 Nup98 7 Nup96 Nup107 8 Nup96 Nup133 9 Nup96 Nup153 10 Nup98 Nup107 11 Nup98 Nup133 12 Nup98 Nup153 13 Nup107 Nup133 14 Nup107 Nup153 15 Nup133 Nup153 Beginning Analysis at 2009/11/5 10:23 COMPARISON_1 Nup75 Nup96 model np lnL yint slope nullA 30 -13030.7 0.0701562 NA nullB 30 -13032 0.0732619 NA END_1 COMPARISON_2 Nup75 Nup98 model np lnL yint slope nullA 30 -13829.6 0.0701745 NA nullB 30 -13838 0.0746634 NA END_2 COMPARISON_3 Nup75 Nup107 model np lnL yint slope nullA 30 -12505.2 0.0701744 NA nullB 30 -12514.1 0.0649846 NA END_3 COMPARISON_4 Nup75 Nup133 model np lnL yint slope nullA 30 -15020.4 0.0701829 NA nullB 30 -15054.8 0.0669783 NA END_4 COMPARISON_5 Nup75 Nup153 model np lnL yint slope nullA 30 -12501.9 0.0701555 NA nullB 30 -12505.2 0.191955 NA END_5 COMPARISON_6 Nup96 Nup98 model np lnL yint slope nullA 30 -15567.3 0.0732539 NA nullB 30 -15574.4 0.0746451 NA END_6 COMPARISON_7 Nup96 Nup107 model np lnL yint slope nullA 30 -14242.9 0.0732535 NA nullB 30 -14250.4 0.0649842 NA END_7 COMPARISON_8 Nup96 Nup133 model np lnL yint slope nullA 30 -16758.1 0.0732629 NA nullB 30 -16791.2 0.0669765 NA END_8 COMPARISON_9 Nup96 Nup153 model np lnL yint slope nullA 30 -14239.6 0.0732545 NA nullB 30 -14241.6 0.191826 NA END_9 COMPARISON_10 Nup98 Nup107 model np lnL yint slope nullA 30 -15048.9 0.0746646 NA nullB 30 -15049.4 0.0649947 NA END_10 COMPARISON_11 Nup98 Nup133 model np lnL yint slope nullA 30 -17564.1 0.0746489 NA nullB 30 -17590.1 0.0669614 NA END_11 COMPARISON_12 Nup98 Nup153 model np lnL yint slope nullA 30 -15045.6 0.0746386 NA nullB 30 -15040.5 0.191905 NA END_12 COMPARISON_13 Nup107 Nup133 model np lnL yint slope nullA 30 -16240.2 0.0649746 NA nullB 30 -16265.7 0.0669625 NA END_13 COMPARISON_14 Nup107 Nup153 model np lnL yint slope nullA 30 -13721.7 0.0649963 NA nullB 30 -13716.1 0.191893 NA END_14 COMPARISON_15 Nup133 Nup153 model np lnL yint slope nullA 30 -16262.4 0.0669801 NA nullB 30 -16231.3 0.191857 NA END_15 Start time: 2009/11/5 10:23 Stop time: 2009/11/5 10:35 Analysis Complete. |
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