[91mrun[0m /tmp/dralph/partis-main/bin/FastTree-linux -gtr -nt -out test/paired/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out test/paired/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa
FastTree Version 2.1.10 SSE3
Alignment: test/paired/new-results/partition-new-simu/fasttree/iclust-1/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 275 times)
Initial topology in 0.00 seconds
Refining topology: 14 rounds ME-NNIs, 2 rounds ME-SPRs, 7 rounds ML-NNIs
Total branch-length 0.271 after 0.03 sec
ML-NNI round 1: LogLk = -2139.116 NNIs 2 max delta 1.19 Time 0.04
GTR Frequencies: 0.2309 0.2546 0.2948 0.2197
GTR rates(ac ag at cg ct gt) 1.2857 1.3276 1.7078 0.7264 0.9455 1.0000
      0.10 seconds: Site likelihoods with rate category 16 of 20
Switched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.693 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 = -2042.199 NNIs 0 max delta 0.00 Time 0.12
Turning off heuristics for final round of ML NNIs (converged)
ML-NNI round 3: LogLk = -2042.199 NNIs 0 max delta 0.00 Time 0.14 (final)
Optimize all lengths: LogLk = -2042.199 Time 0.14
Total time: 0.16 seconds Unique: 11/11 Bad splits: 0/8