Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates a consensus tree. It plots the maximum likelihood tree with bootstrap values, drift and residuals and calculates statistics for every migration event, such as migration support, standard error and p-values.
Even though there are no errors printed when running this script, I am getting empty .llik files. Other files seem to be produced and seem fine. I have succesfully used this data set for a simple treemix analyses, and this issue did not appeared. Any idea of what might be happening? Thanks so much for any insights!
Hi all,
Even though there are no errors printed when running this script, I am getting empty .llik files. Other files seem to be produced and seem fine. I have succesfully used this data set for a simple treemix analyses, and this issue did not appeared. Any idea of what might be happening? Thanks so much for any insights!
Best,
Laura
below the relevant section of the .sbatch script
echo "starting step 1" sh ../scripts/treemix/Step1_TreeMix.sh treemix_data.gz 10 100 miniatus 10 /apps/software/gcc-12.1.0/miniconda3/23.1.0/envs/phylip/exe/consense treemixMyiob 1 3 10