warning - The model you specified on the command line will be ignored
Lída Veselá
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
Lida
p.s.
I am sorry if the message was sent twice
Oleksiy Kozlov
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)
(LG+G+I).
If you want to re-run the analysis from scratch and ignore existing checkpoints, just add "--redo"
to the command line.
Best,
Oleksiy
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