aculasso
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monkey business
Posts: 13
Buenos Aires - Argentina
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Hello!
I'm trying to estimate the sustitution rate of some region of Hepatits C Virus. I've several (7) samples of a patient spanning several years. Up to now I've 2 estimations, one with BEAST using cloned sequences of each sample, and a "quick and dirt" estimation by linear regresion of branch length over time in the best tree (I say "the best", because it was the result of an exhaustive search with the best fit model) of direct sequences (7 taxa). Some time ago I've used DatedTips to estimate this rate which was an order of magnitude less than the other estimations. I'm trying to perform the GADatedClock analysis. I've the sequences, the tree, set local or global estimations, and always get an error:
Expression syntax/semantics error. Current BL Command:ExportAMatrix(modelFile,StringToMatrix(currentPopulation[populationSize-1]),1,1) Current Task has been terminated. Would you like to see the remaining error...
and the program stops.
Here is the output of the console:
What units are the dates measured in (e.g. months. This is only used for reporting the results.)?days Read the following dates: Nov1998_16301: 16301 days Jul1999_16524: 16524 days Mar2000_16772: 16772 days Feb2002_17490: 17490 days Ago2006_19107: 19107 days Oct2001_17356: 17356 days
______________FREE RATES______________ Log Likelihood = -1146.88982261698; Shared Parameters: R=0.494877=0.494877
Tree givenTree=(Nov1998_16301:0.00676707,Jul1999_16524:0,(Mar2000_16772:0.0107896,(Fe b2002_17490:0.00564523,(Ago2006_19107:0.0309347,Oct2001_17356:0.00512011)50:0.00 606189)28:0.0071273)98:0.0200414);
BEST AIC=2313.78 Fitting the single rate model... Pass 1(0) log-L = -1155.32 Pass 2(1) log-L = -1155.32 Pass 3(2) log-L = -1155.32
______________SINGLE RATE______________ Log Likelihood = -1155.32412978027; Shared Parameters: clockTree_scaler_0=0.373943 R=0.494877=0.494877
Tree clockTree=(Nov1998_16301:0.00617536,Jul1999_16524:0.0102448,(Mar2000_16772:0.004 91676,(Feb2002_17490:0.0101288,(Ago2006_19107:0.0357021,Oct2001_17356:0.00374861 )50:0.00393489)28:0.0078905)98:0.00985373);
AIC=2320.65
Starting GA with 2 rate classes Baseline Model Fit c-AIC = 2320.65 Starting the GA now... Generation 2 with 2 rate classes. Best c-AIC found far is 2310.53 This is a 10.1221 improvement over the single-rate model GA has considered 29 unique models so far Total run time so far is 0 hrs 0 mins 4 seconds Average cluster time per generation is 4.00 seconds Average CPU time per model is 0.14 seconds Convergence criterion: 0/50
Other usefull data... Model HKY OS: Windows SP3 HyPhy Version: 1.0020080508
Any suggestions to solve this issue?
Thanks in advance!
Andrés
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