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RAxML_info.bestml
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IMPORTANT WARNING: Sequences SDGD and SDGI are exactly identical
IMPORTANT WARNING
Found 1 sequence that is exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.
An alignment file with sequence duplicates removed has already
been printed to file /projects/tallis/binghui2/19fa/large_aligments/datasets/500M1/R0/rose.aln.true.fasta.reduced
Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs"
This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Sarah Lutteropp (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Charlie Taylor (UF)
Alignment has 2105 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 65.56%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 1 inferences on the original alignment using 1 distinct randomized MP trees
All free model parameters will be estimated by RAxML
GAMMA model of rate heterogeneity, ML estimate of alpha-parameter
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 2105
Name: No Name Provided
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
./raxmlHPC-PTHREADS-SSE3 -s /projects/tallis/binghui2/19fa/large_aligments/datasets/500M1/R0/rose.aln.true.fasta -p 1 -w /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M1/R0/ -m GTRGAMMA -T 5 -n bestml
Partition: 0 with name: No Name Provided
Base frequencies: 0.252 0.247 0.249 0.252
Inference[0]: Time 907.119090 GAMMA-based likelihood -446312.714729, best rearrangement setting 10
alpha[0]: 0.913013 rates[0] ac ag at cg ct gt: 1.198555 3.453825 0.504151 1.105234 4.352406 1.000000
Conducting final model optimizations on all 1 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -446312.689647 tree written to file /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M1/R0/RAxML_result.bestml
Starting final GAMMA-based thorough Optimization on tree 0 likelihood -446312.689647 ....
Final GAMMA-based Score of best tree -446312.689647
Program execution info written to /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M1/R0/RAxML_info.bestml
Best-scoring ML tree written to: /projects/tallis/binghui2/19fa/large_aligments/raxml_results/500M1/R0/RAxML_bestTree.bestml
Overall execution time: 1153.568464 secs or 0.320436 hours or 0.013351 days