[91mrun[0m /home/dralph/work/partis/bin/FastTree-linux -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 2.1.10 SSE3
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 156 times)
Initial topology in 0.00 seconds
Refining topology: 14 rounds ME-NNIs, 2 rounds ME-SPRs, 7 rounds ML-NNIs
Total branch-length 0.316 after 0.03 sec
ML-NNI round 1: LogLk = -2186.327 NNIs 0 max delta 0.00 Time 0.05
GTR Frequencies: 0.2427 0.2641 0.2808 0.2124
GTR rates(ac ag at cg ct gt) 0.8463 0.7269 0.8747 0.8623 0.8871 1.0000
      0.10 seconds: Site likelihoods with rate category 20 of 20
Switched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.698 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 = -2112.731 NNIs 0 max delta 0.00 Time 0.11
Turning off heuristics for final round of ML NNIs (converged)
ML-NNI round 3: LogLk = -2112.717 NNIs 0 max delta 0.00 Time 0.13 (final)
Optimize all lengths: LogLk = -2112.717 Time 0.13
Total time: 0.16 seconds Unique: 12/12 Bad splits: 0/9