Unable to reconstruct phylogenetic trees using Beast

bioDS / phyloRNAanalysis

A phylogenetic analysis from scRNA-seq data using both expression levels and identified SNVs

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Unable to reconstruct phylogenetic trees using Beast #1

Open nieyuan1027 opened 3 years ago

nieyuan1027 commented 3 years ago

Hi I am trying to reconstruct phylogenetics using BEAST2 on linux. The code and data comes from 'run_wang2021.r'. Now,I am getting this error: 1623226851

The test code is as follows: beasts( patient_fasta, template = file.path("/Public/Script/shouhou/phyloRNA/phyloRNAanalysis-master/templates", "BDStrictOrdinal.xml"), outdir = file.path(outdir, patient, "BI") ) I'm wondering if there are some packages I have not installed.

Thanks for your help. Best, Nie Yuan

J-Moravec commented 3 years ago

Hi Nie, looks like you are missing some BEAST packages, specifically the MM package that contains the ordinal model.

Please, type (if you are on Linux and have BEAST2 installed):

packagemanager -add MM

That should download the MM package and its dependencies.

You can also do this through GUI in Beauti. https://beast2.blogs.auckland.ac.nz/managing-packages/

nieyuan1027 commented 3 years ago

@J-Moravec，Thanks for the hint! The problem solved after installing the MM package.