draw bipartition information

[Abush zinaw Zergabachew]

I was trying to draw bipartition information on a tree (provided with -t ) based on multiple trees (specified by -z) using command;

raxmlHPC -N 1000 -T 4 -f b -m GTRCAT -z Trees/Menthinae_bootstrap.All -t Trees/Menthinae_dist_matx_cor_.tre -n BS_TREE_MAIN

but keep getting Computation of bipartitions (-f b) not implemented for the MPI-Version error.

I am using the hybrid version RAxML/8.2.12-foss-2018b-hybrid-avx2 of RAxML on our cluster.

Script:

#!/bin/sh

#SBATCH --job-name=raxml

#SBATCH --account=nn9370k

#SBATCH -o log/rax-%j.out

#SBATCH -e log/rax-%j.err

#SBATCH --time=00:30:00

#SBATCH --ntasks=

#SBATCH --mem=8G

## load necessary modules

module purge

module load RAxML/8.2.12-foss-2018b-hybrid-avx2

## draw bipartition information on a tree

raxmlHPC -N 1000 -T 4 -f b -m GTRCAT -z Trees/Menthinae_bootstrap.All -t Trees/Menthinae_dist_matx_cor_.tre -n BS_TREE_MAIN

Please if you have any suggestion; I am not that fluent on bioinformatic so need your help.

Best,

Abush

[Alexandros Stamatakis]

Just run the sequential RAxML version, the draw bipartition function is
very fast to compute and does not require the parallel version anyway,

Alexis

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas

www.exelixis-lab.org

[Mac]

Thank you Alexis,

Sorry, but how can I invoke the sequential RAxML version? I tried raxmlHPC -SSE3, however, still get the same message.

Best,
Abush

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[Alexandros Stamatakis]

you will have to re-compile RAxML to get the seq. version,

Alexis

[Mac]

Solved!

Thanks a lot.
Best,
Abush

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