[91mrun[0m /Users/runner/work/partis/partis/bin/FastTree-macos -gtr -nt -out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/fasttree/iclust-0/input-seqs.fa
FastTree Version 2.2.0 Double precision
Alignment: /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igh/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 24 times)
Initial topology in 0.00 seconds
Refining topology: 12 rounds ME-NNIs, 2 rounds ME-SPRs, 6 rounds ML-NNIs
Total branch-length 0.217 after 0.00 sec
ML-NNI round 1: LogLk = -1009.286 NNIs 0 max delta 0.00 Time 0.01
GTR Frequencies: 0.2219 0.2395 0.3219 0.2167
GTR rates(ac ag at cg ct gt) 0.9477 0.4171 1.2893 0.8129 0.9896 1.0000
Switched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.678 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 = -968.458 NNIs 0 max delta 0.00 Time 0.04
Turning off heuristics for final round of ML NNIs (converged)
ML-NNI round 3: LogLk = -968.419 NNIs 0 max delta 0.00 Time 0.05 (final)
Optimize all lengths: LogLk = -968.417 Time 0.05
Total time: 0.07 seconds Unique: 8/8 Bad splits: 0/5