[Primeusers] Release 1.0 of PrimeGSR

Filipe Garrett fgarret at ub.edu
Thu Feb 12 12:48:02 CET 2009


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
>>>
>>>     
>>   
> 
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-- 
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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