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BDI-pathogens / phyloscanner

Phylogenetics between and within hosts at once, all along the genome.
GNU General Public License v3.0
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Error with analysing own trees (not made with phyloscanner_make_trees.py) #58

Closed Steven-Kemp closed 3 years ago

Steven-Kemp commented 3 years ago

When attempting to analyse my own trees (constructed with MrBayes or IQTREE) I keep bumping into an error with ptrees[[id]].

Using the following command: ./phyloscanner_analyse_trees.R /Users/steve/pangea_SA.tree pangea_out s,12.5 --outgroupName AF411967_FULL --multifurcationThreshold g

The following issue presents:

Random number seed is 894343788 Error in ptrees[[id]] <- ptree : attempt to select less than one element in integerOneIndex Calls: phyloscanner.analyse.tree ... phyloscanner.analyse.trees -> initialise.phyloscanner Execution halted

Any idea what it might not like?

Best wishes, Steve