[91mrun[0m /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out test/paired/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out test/paired/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
FastTree Version 2.2.0 Double precision
Alignment: test/paired/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa
Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Generalized Time-Reversible, CAT approximation with 20 rate categories
Ignored unknown character X (seen 132 times)
Initial topology in 0.00 seconds
Refining topology: 10 rounds ME-NNIs, 2 rounds ME-SPRs, 5 rounds ML-NNIs
Total branch-length 0.072 after 0.00 sec
ML-NNI round 1: LogLk = -1300.628 NNIs 1 max delta 1.15 Time 0.01
GTR Frequencies: 0.2567 0.2538 0.2729 0.2166
GTR rates(ac ag at cg ct gt) 0.8073 1.2192 0.7088 1.1279 0.4727 1.0000
Switched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.641 so that average rate = 1.0
CAT-based log-likelihoods may not be comparable across runs
Use -gamma for approximate but comparable Gamma(20) log-likelihoods
ML-NNI round 2: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.03
Turning off heuristics for final round of ML NNIs (converged)
ML-NNI round 3: LogLk = -1274.638 NNIs 0 max delta 0.00 Time 0.04 (final)
Optimize all lengths: LogLk = -1274.638 Time 0.04
Total time: 0.06 seconds Unique: 6/6 Bad splits: 0/3