[Primeusers] PrimeGSR optimization with fixed tree

[Jacky Hess]

Hi Lars,

I'm using the following command line:

primeGSR -o 672.reconciled.prime -i 100000 -t 100 -Sm JTT -Sn 4 -Ed 
Gamma -Hi species_tree.tree -Gi 672_reconciled.nwk -Gg 
672_chopped_slim.fas 672_seq_map_mapping.txt

Thanks,

Jacky

Lars Arvestad wrote:
> Hi Jacky,
> Could you please send the command line that you are actually executing?
>    
>     Lars
>
>
> Jacky Hess wrote:
>   
>> Hello,
>>
>> I am trying to run primeGSR on a fixed gene tree to estimate the maximum 
>> a posteriori probability but it looks like the optimization is stuck and 
>> never really goes beyond the first set of values.
>>
>> Also I receive the following error messages which I suspect are related 
>> to this:
>>
>> # Tried to set length of node 17 to 0 which is less than minimum 
>> 4.45015e-308
>>
>> etc.
>>
>> Does anyone know what might be going wrong here?
>>
>> Thanks very much,
>>
>> Jacky
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>>     
>
>
>