[Primeusers] Release 1.0 of PrimeGSR

[Lars Arvestad]

What scale did you try? If you haven't already, try scaling the tree so 
the root is at 1.0.

    Lars


Filipe Garrett wrote:
>
> 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
>>>>>>
>>>>>>             
>>>>>         
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>>>> Primeusers at sbc.su.se
>>>> https://mail.sbc.su.se/mailman/listinfo/primeusers
>>>>
>>>>     
>>>   
>>
>>
>
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-- 
School of Computer Science and Communication
and Stockholm Bioinformatics Center
http://www.csc.kth.se/~arve