Starting trees

Patrik Medstrand

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Oct 10, 2021, 1:28:19 PM10/10/21

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Thanks for providing raxml! I have a question related to starting trees:

Below I ask for five random parsimony starting trees --tree pars{5}, but seems to be ignored - I believe 10 is used instead.

so for this run, which was intended to run a total of 5*20 trees (=100), I got 10*20=200 trees.

Any idea why I get 200 trees instead of 100?

Thank you very much

/patrik

commands for running on a cluster

#!/bin/bash -l

#SBATCH -A my-id

#SBATCH -p node -n 20

#SBATCH -t 1-00:00:00

#SBATCH -J raxml-test

module load bioinfo-tools

module load RAxML-NG/0.9.0

module load gnuparallel

parallel --jobs 10 raxml-ng --threads 2 --msa T2.raxml.rba --tree pars{5} --prefix T{} --seed {} ::: $(seq 1 20)

Alexey Kozlov

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Oct 12, 2021, 12:42:18 AM10/12/21

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Hi Patrik,

you have rather complicated parallelization setup which apparently does not work as intended.

I recommend upgrading to the latest raxml-ng v.1.0.3 which supports parallelization across tree
searches out-of-the-box.

Best,
Alexey

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Patrik Medstrand

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Oct 12, 2021, 9:34:53 AM10/12/21

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Thanks a lot for your response! I will ask the administrators to make v.1.0.3 available