Firstly, the check function is sucessfully performed with the following command:
raxml-ng --msa check-final-merge.min4.fasta --model TVM+I+G4 --check --prefix check
Then I run the following command to make the ML tree:
raxml-ng --msa check-final-merge.min4.fasta --model TVM+I+G4 --all --bs-trees 100 --threads 85 --prefix tree
Following is the log:
Analysis options:
run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)
start tree(s): random (10) + parsimony (10)
bootstrap replicates: 100
random seed: 1676688219
tip-inner: OFF
pattern compression: ON
per-rate scalers: OFF
site repeats: ON
branch lengths: proportional (ML estimate, algorithm: NR-FAST)
SIMD kernels: AVX2
parallelization: coarse-grained (auto), PTHREADS (85 threads), thread pinning: OFF
[00:00:00] Reading alignment from file: check-final-merge.min4.fasta
[00:00:00] Loaded alignment with 285 taxa and 228714 sites
Alignment comprises 1 partitions and 59569 patterns
Firstly, the check function is sucessfully performed with the following command: raxml-ng --msa check-final-merge.min4.fasta --model TVM+I+G4 --check --prefix check
Then I run the following command to make the ML tree: raxml-ng --msa check-final-merge.min4.fasta --model TVM+I+G4 --all --bs-trees 100 --threads 85 --prefix tree
Following is the log: Analysis options: run mode: ML tree search + bootstrapping (Felsenstein Bootstrap) start tree(s): random (10) + parsimony (10) bootstrap replicates: 100 random seed: 1676688219 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (85 threads), thread pinning: OFF
[00:00:00] Reading alignment from file: check-final-merge.min4.fasta [00:00:00] Loaded alignment with 285 taxa and 228714 sites
Alignment comprises 1 partitions and 59569 patterns
Partition 0: noname Model: TVM+FO+I+G4m Alignment sites / patterns: 228714 / 59569 Gaps: 1.09 % Invariant sites: 65.21 %
NOTE: Binary MSA file created: check-final-merge.min4.fasta.raxml.rba
Parallelization scheme autoconfig: 5 worker(s) x 17 thread(s)
Parallel reduction/worker buffer size: 1 KB / 0 KB
[00:00:01] Generating 10 random starting tree(s) with 285 taxa [00:00:01] Generating 10 parsimony starting tree(s) with 285 taxa [00:00:31] Data distribution: max. partitions/sites/weight per thread: 1 / 3505 / 56080 [00:00:31] Data distribution: max. searches per worker: 24
Starting ML tree search with 20 distinct starting trees
Best wishes!