[Primeusers] Release 1.0 of PrimeGSR

[Lars Arvestad]

Hi Filipe,
Please try the option "-c 50", and if the problem persists, double the 
number. This option decides how many discretization points we will use 
in the speciation tree. If there are too few points, there will be edges 
in the species tree where we can't put down a gene tree node, even if we 
need to. Unfortunately, we do not detect and fix this properly yet.

    Best regards,
    Lars


Filipe Garrett skrev:
> Dear Lars,
>
> Despite not knowing what it was, I've been a able to fix the previous error ("not a valid alphabet 
> state") by remaking the input files (probably some typo).
> However a new error occurs:
> "
> Error:
>      Probability: Division with zero attempted!
> "
>
> Any idea of what may be?
> thanks in adv,
> FG
>
>
> Lars Arvestad wrote:
>   
>>> I've just installed primeGSR and had some problems. It couldn't find the "g2f" library. I removed it 
>>> from the Makefile and it compiled without errors. Run the sample files and everything perfect (at 
>>> least I think since I don't know if the output is correct). What is the function of this library? Is 
>>> it normal to compile without it?
>>>   
>>>       
>> Do you mean "g2c"? This used to be needed when linking the linear 
>> algebra libraries BLAS and LAPACK. Maybe this need has disappeared in 
>> modern systems. I will remove it from the makefile!
>>
>>     
>>> Then I was trying primeGSR and managed to input everything correctly (I think). However an error 
>>> occurred stating:
>>>
>>> "
>>> the state  is notError:
>>>      not a valid alphabet state
>>> "
>>>
>>> I'm using this command line on a PC Fedora Core 7 Linux:
>>> primeGSR -d -o output.mcmc -Bp 0.1 0.1 -Ed Gamma -i 1000 -t 10 -Sm JTT -Hi tree.nwk in_seq.fas in_seq.gs
>>>       
>> This bad error message is due to finding an unrecognized/unsupported 
>> character in the sequence data. If you have trouble finding the 
>> offending sequence, send it to me and I will take a look at it.
>>
>> Thanks for the bug reports!
>> Lasse
>>
>>     
>
>