warning - The model you specified on the command line will be ignored

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Lída Veselá

Jun 10, 2024, 8:54:46 AMJun 10
to raxml

Dear all,


I would like to ask you for advice. I have 401 protein sequences alignment after trimm. According to Modeltest I decide for LG+I+G4 model. So I ran Raxml-ng with this command:

 ../soft/raxml/raxml-ng --seed 568317 --all --msa ARE5_dataset_20240529_optimalizace\(45\).mafft.trimmed04 --model LG+I+G4 --tree pars{100},rand{100} --bs-trees 200


The run was finished but in log file I found warning (see below). I am confused because in MSA is only FASTA format of alignment without model. And I am not sure which model at the end Raxml-ng used. Can you explain to me what is wrong?


RAxML-NG v. 1.2.2-master released on 30.04.2024 by The Exelixis Lab.

Developed by: Alexey M. Kozlov and Alexandros Stamatakis.

Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth, Julia Haag, Anastasis Togkousidis.

Latest version: https://github.com/amkozlov/raxml-ng

Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml


System: (not found), 10 cores, 7 GB RAM


RAxML-NG was called at 04-Jun-2024 15:57:33 as follows:


../soft/raxml/raxml-ng --seed 568317 --all --msa ARE5_dataset_20240529_optimalizace(45).mafft.trimmed04 --model LG+I+G4 --tree pars{100},rand{100} --bs-trees 200


Analysis options:

  run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)

  start tree(s): random (100) + parsimony (100)

  bootstrap replicates: parsimony (200)

  random seed: 568317

  tip-inner: OFF

  pattern compression: ON

  per-rate scalers: OFF

  site repeats: ON

  logLH epsilon: general: 10.000000, brlen-triplet: 1000.000000

  fast spr radius: AUTO

  spr subtree cutoff: 1.000000

  fast CLV updates: ON

  branch lengths: proportional (ML estimate, algorithm: NR-FAST)

  SIMD kernels: SSE3

  parallelization: coarse-grained (auto), PTHREADS (auto)


WARNING: The model you specified on the command line (LG+I+G4) will be ignored

         since the binary MSA file already contains a model definition.

         If you want to change the model, please re-run RAxML-NG

         with the original PHYLIP/FASTA alignment and --redo option.


[00:00:00] Loading binary alignment from file: ARE5_dataset_20240529_optimalizace(45).mafft.trimmed04.raxml.rba

[00:00:00] Alignment comprises 401 taxa, 1 partitions and 532 patterns


Partition 0: noname

Model: LG+I+G4m

Alignment sites / patterns: 538 / 532

Gaps: 2.46 %

Invariant sites: 5.76 %



Parallelization scheme autoconfig: 5 worker(s) x 2 thread(s)


Parallel reduction/worker buffer size: 1 KB  / 0 KB


[00:00:00] NOTE: Resuming execution from checkpoint (logLH: -149063.58, ML trees: 10, bootstraps: 0)

[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 266 / 21280

[00:00:00] Data distribution: max. searches per worker: 78


 Thank you very much


Best regards


I am sorry if the message was sent twice

Oleksiy Kozlov

Jun 10, 2024, 9:40:31 AMJun 10
to ra...@googlegroups.com
Dear Lida,

there is nothing wrong with this run, it just automatically restarted from a checkpoint, as you can
see from the following line:

[00:00:00] NOTE: Resuming execution from checkpoint (logLH: -149063.58, ML trees: 10, bootstraps: 0)

If it was intended, no problem, since models in the checkpoint and on the command line are identical

If you want to re-run the analysis from scratch and ignore existing checkpoints, just add "--redo"
to the command line.

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Lída Veselá

Jun 11, 2024, 4:36:30 AMJun 11
to raxml
Dear Oleksiy, 

thank you very much for fast help and verification, that run was without problems.


Dne pondělí 10. června 2024 v 15:40:31 UTC+2 uživatel Oleksiy Kozlov napsal:
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