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HYPHY Package >> HyPhy bugs >> a different freezing problem http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1295291822 Message started by jssdenton on Jan 17th, 2011 at 11:17am |
Title: a different freezing problem Post by jssdenton on Jan 17th, 2011 at 11:17am
Hi folks.
I'm running HyPhy 2.0 on OSX 10.6.6, and trying to do a partitionwise model selection using nucmodelcompare.bf and a user-input tree topology (I removed the branch lengths). The dataset is 196 taxa and 4833 bp total, or 4833/3 for each partition. I try to run nucmodelcompare, and HyPhy freezes. Freezing occurs generally after the initial likelihood calculation of the (012345) GTR model. Is there a best way to specify a partitionwise model test in HyPhy? Could that be the problem? I have a SETS block in my NEXUS file. The file is attached. Thanks! ~John |
Title: Re: a different freezing problem Post by Sergei on Jan 19th, 2011 at 12:01pm
Hi John,
The default version of 'nucmodelcompare.bf' does not perform partition-based testing, as far as I recall. Did you modify the file -- if som please attach it for me to try to recreate the issue. Otherwise, could you please list the options you were feeding in to the analysis? Sergei |
Title: Re: a different freezing problem Post by jssdenton on Jan 20th, 2011 at 9:19am
Hi Sergei,
Thanks. I did not modify the nucmodelcompare.bf script. What I was going to try to do was to use a SETS block to define a single codon position and make three files--one for 1st position, one for 2nd position, and one for 3rd position and run them separately. The entire dataset would be there each time, but only an individual partition would be assigned. I was assuming that HyPhy would then only fit a model to the defined partition. The guide tree I was using is a NJ tree built with GY94 distances (output from HyPhy). I was going to use this tree for fitting all partitions. The options I used for nucmodelcompare did not alter the freezing. What I tried most frequently were nucmodelcompare->global w/variation->every time->gamma->4->input NEXUS+tree->alpha=0.05 I have attached a zip of the file + tree. Thanks! http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=Gobystops2_1_nex.zip (179 KB | )
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Title: Re: a different freezing problem Post by jssdenton on Jan 21st, 2011 at 12:42pm
Hi Sergei,
I am using 32-bit OSX 10.6.6 and the version of HyPhy 2.0 based on a previous post in the forum from Dec 23rd, I think. Thanks for the paper. I am using the codon position approximation given the size of the dataset. Do you have any recommendations on how to generate the datasets of individual positions? I had used an 'exclude' command for regular modeltest-like implementations. |
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