Dear all,

I am a new user of HyPhy and really excited about its possibilities, but as a beginner I have several problems running the analyses that I would like to. And to start with, the most simple one is that when I’m trying to restore my NucleotideModelFit (eg during Standard Analysis/Positive selection/Quick Selection Detection) I get this message indicated below. To me this indicates that there is something wrong with the partition, although I can’t find out what. I’ve been over and over again the manual (also the one included in the Phylogenetics Handbook), exported and saved the NucModelFit analysis and the Partition in all possible ways, but I still can’t get over this simple step.

Thanks in advance for your support.

Kind regards
Ioannis
 

Error:DataSet/DataSetFilter nucData has not been initialized
Call stack
1 : Harvest Frequencies into matrix positionFrequencies from DataSet nucData with unit size = 3 with atom size = 1 with position specific flag = 1 Partition:

Hi Ioannis,

The only fits that you can reload for QuickSelectionDetection analyses are the ones created by the same analysis (i.e. QuickSelectionDetection and 'New Analysis'). If you run AnalyzeNucData.bf (or other analyses), object naming, modeling assumptions etc can not be expected to match what QuickSelectionDetection expects.

Sergei