[91mrun[0m /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out test/paired/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out test/paired/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa
FastTree Version 2.2.0 Double precision
Alignment: test/paired/new-results/partition-new-simu/fasttree/iclust-0/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 32 times)
Initial topology in 0.00 seconds
Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
Total branch-length 0.172 after 0.01 sec
ML-NNI round 1: LogLk = -1718.230 NNIs 0 max delta 0.00 Time 0.05
GTR Frequencies: 0.2101 0.3021 0.2760 0.2118
GTR rates(ac ag at cg ct gt) 1.2927 1.2254 1.4006 0.7465 1.0327 1.0000
Switched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.666 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 = -1660.926 NNIs 0 max delta 0.00 Time 0.10
Turning off heuristics for final round of ML NNIs (converged)
      0.10 seconds: ML NNI round 3 of 6, 1 of 6 splits
ML-NNI round 3: LogLk = -1660.925 NNIs 0 max delta 0.00 Time 0.12 (final)
Optimize all lengths: LogLk = -1660.925 Time 0.12
Total time: 0.14 seconds Unique: 8/8 Bad splits: 0/5