Bali-Phy bp-analyze bug report

[Cristian Sharma]

Hi Ben,

I am using bp-analyze to check if my runs have converged by running it as so:

bp-analyze run-*

(I have three runs going named run-1, run-2,run-3)

When I run bp-analyze I get the following error message:

Generate mixing diagnostics for topologies ...command: '/usr/bin/R' '--slave' '--vanilla' '--args' 'Results/LOD-table' 'Results/convergence1-PP.svg' 'Results/convergence2-PP.svg' < '/usr/local/bali-phy-3.6.0/lib/bali-phy/libexec/compare-runs2.R'

 exit: 1

And from the resulting commands.log file:

err: Error in xtfrm.data.frame(x) : cannot xtfrm data frames

Calls: sort ... lapply -> FUN -> as.vector -> xtfrm -> xtfrm.data.frame

Execution halted

 exit: 1

  err: Error in xtfrm.data.frame(x) : cannot xtfrm data frames

Calls: sort ... lapply -> FUN -> as.vector -> xtfrm -> xtfrm.data.frame

Execution halted

The Results/ directory that is generated contains MAP and consensus trees but no alignments and no index.html file.

I am using bali-phy version 3.6.1.

Best,

Crís Sharma

--

Crístían V.R. Sharma (he/him)

PhD. Candidate in Biochemistry and Biophysics

Theobald Lab, Brandeis University

Graduate School of Art and Sciences

cristia...@brandeis.edu