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carolindahms / TreeMix

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.
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Step3_TreeMix.sh gets stuck #6

Open Yyeserin opened 1 year ago

Yyeserin commented 1 year ago

Hello,

I am running the Step3_TreeMix.sh with m=4. I use this code:

sh Step3_TreeMix.sh nomissing.populations.treemix.gz 6 1 noRoot 300 4 m4 100 Step1_out/nomissing.4_outtree.newick /home/yeserin/snphylo/phylip-3.697/exe/consense

It works well when I use m=3. But for m=4, it gets stuck for hours while doing the last bootstraps. It doesn't progress at all. Othersie, it runs fast until the very last bootstraps. Is it normal? Should I wait a few days to see if the analysis finishes or not?

Best, Yeserin.

bshahid5 commented 1 year ago

hi Yeserin, Im having a similar problem. Were you able to figure out how to get it not to get stuck?

-Bushra