Can I use -cal with PhyloBayes-MPI for time calibrated tree reconstruction?

[Ruiqi-CUB]

I was trying to use PhyloBayes-MPI with a large dataset. Thanks for developing this awesome tool!

However, I encountered a problem while trying to get time calibrated with "mpirun -np 20 pb_mpi", I checked the documentation of PhyloBayes-MPI, it seems that I can't use the -cal flag for time calibration. Is that correct? If so, should I get the consensus tree first with mpi, then use the consensus tree to run PhyloBayes on a single node with less iterations to get it calibrated?

Thanks a lot! Please see my code and returned message from terminal below. Code (just run 2 iterations to check): mpirun -np 20 pb_mpi -cat -gtr -x 1 2 -d PHYLIP -T MYTREE -r OUTGROUP -cal CALFILE -ln treecalib.CAT_GTR.chain0

The terminal just returns with all the flag options with the following:

Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted.

---

mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:

Process name: [[16724,1],1] Exit code: 1

Thanks a lot!

[bayesiancook]

Dear Ruiqi,

pbmpi does not implement molecular dating. Only the original non-mpi version of phylobayes does (bayesiancook/phylobayes.git). The MPI version was meant to be specialized for more efficient phylogenetic estimation, leaving out all other options of the original version.

of note, if your dataset is large in terms of number of aligned positions, you could certainly try to run a dating analysis with a smaller number of positions.

I hope this helps,

best,

bc.

[Ruiqi-CUB]

Thanks a lot for your quick reply. After I use the MPI version, may I use the original version just for time calibration? Since the tree topology is fixed, I guess it doesn't need tons of iterations? For example, after running 50k iterations from the mpi version, then I use the consensus tree from the results to run the original version 10k iterations just for time calibration, does it work this way?

Thanks Ruiqi

On Fri, Jan 27, 2023 at 1:26 PM bayesiancook @.***> wrote:

Dear Ruiqi,

pbmpi does not implement molecular dating. Only the original non-mpi version of phylobayes does (bayesiancook/phylobayes.git). The MPI version was meant to be specialized for more efficient phylogenetic estimation, leaving out all other options of the original version.

of note, if your dataset is large in terms of number of aligned positions, you could certainly try to run a dating analysis with a smaller number of positions.

I hope this helps,

best,

bc.

— Reply to this email directly, view it on GitHub https://github.com/bayesiancook/pbmpi/issues/33#issuecomment-1407039876, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALEILISVNEJDC5X56L3FXMDWUQVPDANCNFSM6AAAAAAUJAK6UI . You are receiving this because you authored the thread.Message ID: @.***>

-- Ruiqi Li PhD Candidate Dept. of Ecology and Evolutionary Biology University of Colorado Boulder [image: A button with "Hear my name" text for name playback in email signature] https://www.name-coach.com/ruiqi-li

[bayesiancook]

you can certainly proceed in two steps

• first inferring the tree using the mpi version
• the dating it using the non mpi one.

you will still need many iterations for the dating step.

on the other hand: perhaps you don’t need a very large number of aligned positions. I don’t know how large your data set currently is (how many sites, how many taxa), but perhaps you want to first try with data of reasonable size (~10 000 positions) before doing a bigger analysis.

best,

Nicolas

Le 27 janv. 2023 à 23:14, Ruiqi-CUB @.***> a écrit :

Thanks a lot for your quick reply. After I use the MPI version, may I use the original version just for time calibration? Since the tree topology is fixed, I guess it doesn't need tons of iterations? For example, after running 50k iterations from the mpi version, then I use the consensus tree from the results to run the original version 10k iterations just for time calibration, does it work this way?

Thanks Ruiqi

On Fri, Jan 27, 2023 at 1:26 PM bayesiancook @.***> wrote:

Dear Ruiqi,

pbmpi does not implement molecular dating. Only the original non-mpi version of phylobayes does (bayesiancook/phylobayes.git). The MPI version was meant to be specialized for more efficient phylogenetic estimation, leaving out all other options of the original version.

of note, if your dataset is large in terms of number of aligned positions, you could certainly try to run a dating analysis with a smaller number of positions.

I hope this helps,

best,

bc.

— Reply to this email directly, view it on GitHub https://github.com/bayesiancook/pbmpi/issues/33#issuecomment-1407039876, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALEILISVNEJDC5X56L3FXMDWUQVPDANCNFSM6AAAAAAUJAK6UI . You are receiving this because you authored the thread.Message ID: @.***>

-- Ruiqi Li PhD Candidate Dept. of Ecology and Evolutionary Biology University of Colorado Boulder [image: A button with "Hear my name" text for name playback in email signature] https://www.name-coach.com/ruiqi-li — Reply to this email directly, view it on GitHub https://github.com/bayesiancook/pbmpi/issues/33#issuecomment-1407129974, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB6ARIGR4OBPZQFLMA2DOXLWURCDXANCNFSM6AAAAAAUJAK6UI. You are receiving this because you commented.