[Primeusers] Release 1.0 of PrimeGSR

[Lars Arvestad]

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
>>
>>     
>
>   


-- 
School of Computer Science and Communication
and Stockholm Bioinformatics Center
http://www.csc.kth.se/~arve