[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-igk/fasttree/iclust-1/fasttree.out /Users/runner/work/partis/partis/test/paired/new-results/partition-new-simu/igh+igk/partition-igk/fasttree/iclust-1/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-igk/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 30 times)
Initial topology in 0.00 seconds
Refining topology: 4 rounds ME-NNIs, 2 rounds ME-SPRs, 2 rounds ML-NNIs
Total branch-length 0.003 after 0.00 sec
ML-NNI round 1: LogLk = -458.427 NNIs 0 max delta 0.00 Time 0.00
Turning off heuristics for final round of ML NNIs
GTR Frequencies: 0.2813 0.2584 0.2294 0.2309
GTR rates(ac ag at cg ct gt) 1.0000 398.8171 1.0000 1.0000 1.0000 1.0000
Switched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.624 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 = -455.146 NNIs 0 max delta 0.00 Time 0.00
Turning off heuristics for final round of ML NNIs (converged)
Optimize all lengths: LogLk = -455.146 Time 0.00
Total time: 0.01 seconds Unique: 2/8 Bad splits: 0/0