[Primeusers] Release 1.0 of PrimeGSR

[Filipe Garrett]

I've just noticed that I've been using a larger species tree (with some species that have no genes 
in the MSA file) but I don't think that was a problem since the error persisted after correcting the 
tree.
I'm sending you the tree I've used now with 11 species; the distances are in millions of years.
I later thought that the large tree branches (in million of years) could be a problem but reducing 
branch length didn't solve the errors.

FG



Lars Arvestad wrote:
> Would you mind sending me the species tree? It would be nice to try to 
> understand it a bit better. I don't think 90 sequences should be a 
> problem, but we have not tried the program with 375 sequences. If the 
> branches in the species tree are very short, then our discretization 
> approach might not work very well.
> 
>     Lars
> 
> 
> 
> Filipe Garrett wrote:
>> Dear Lars,
>>
>> I've tried the "-c 50" option but still the same error.
>> I tried other values of "-c" ranging from 50 to 1000 and all values up to "-c 800" had the same error:
>> "
>> Error:
>>      Probability: Division with zero attempted!
>> "
>>
>> The only case where the program seemed to be working was for "-c 850" but it used way too much 
>> memory: around 11Gb!!!
>>
>> I suppose that's why when I used "-c 900" and "-c 1000" a different error appeared, probably due to 
>> memory limitations:
>> "
>> ...
>> # start init fastGEM_BirthDeathProbs
>> # end init fastGEM_BirthDeathProbs
>>   Exception
>> St9bad_alloc
>> "
>>
>> At this point I think I may have a case of too many sequences/species or low memory. I'm running 
>> primeGSR on a PC Linux machine with 12Gb of RAM and I have 90 sequences from 21 species (also have 
>> another dataset with 375 sequences from 21 species).
>> What do you think?
>>
>> thanks a lot for your time,
>> FG
>>
>>
>> Lars Arvestad wrote:
>>   
>>> 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
>>>>>
>>>>>     
>>>>>         
>>>>   
>>>>       
>>> _______________________________________________
>>> Primeusers mailing list
>>> Primeusers at sbc.su.se
>>> https://mail.sbc.su.se/mailman/listinfo/primeusers
>>>
>>>     
>>   
> 
> 

-- 
Filipe G. Vieira
Departament de Genetica
Universitat de Barcelona
Av. Diagonal, 645
08028 Barcelona
SPAIN
Phone: +34 934 035 306
Fax: +34 934 034 420
fgarret at ub.edu
http://www.ub.edu/molevol/
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