raxml-ng not starting with defined starting tree number?

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Andrew ODonnell

Mar 8, 2024, 1:55:59 PMMar 8
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Hi everyone,

I've been going through the tutorial with my data set to try to explore increasing amounts of tree space to explore. In the fourth part of the tutorial, it suggests to increase the number of starting random trees from the default 10 parsimony + 10 random to 25 each.

I don't think I have the computational resources for 25, so I tried with 15. As you can see below, I set the number of parsimony and random trees each to 15, but the parameters as seen in the Analysis options of the .log file say that I'm only using 10 random and 10 parsimony trees. Did I do something wrong, or am I otherwise missing the point?

Thank you!

RAxML-NG v. 1.1.0 released on 29.11.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) CPU E5-2683 v4 @ 2.10GHz, 32 cores, 503 GB RAM

RAxML-NG was called at 06-Mar-2024 09:56:09 as follows:

raxml-ng-mpi --msa hits.phy --model JTT+G --prefix T4 --threads 32 --seed 2 pars{15},rand{15}

Analysis options:
  run mode: ML tree search
  start tree(s): random (10) + parsimony (10)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (32 threads), thread pinning: ON

[00:00:00] Reading alignment from file: hits.phy
[00:00:00] Loaded alignment with 1637 taxa and 7894 sites

Oleksiy Kozlov

Mar 8, 2024, 2:49:56 PMMar 8
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Hi Andrew,

you forgot the "--tree" flag :)

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Mar 9, 2024, 10:02:24 AMMar 9
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Wow... that was silly of me. Thanks for your quick reply!

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