FastTree Version 2.1.11 Double precision (No SSE3)
Alignment: roaryresult/core_gene_alignment.aln
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
Initial topology in 24.29 secondshits for 1 of 34 seqs
Refining topology: 20 rounds ME-NNIs, 2 rounds ME-SPRs, 10 rounds ML-NNIs
Total branch-length 0.067 after 279.50 sec 1 of 32 splits
ML-NNI round 1: LogLk = -4294141.116 NNIs 8 max delta 2413.17 Time 461.72
GTR Frequencies: 0.2964 0.1899 0.2146 0.2992ep 12 of 12
GTR rates(ac ag at cg ct gt) 1.1495 4.9822 0.9215 0.9770 7.1425 1.0000
Switched to using 20 rate categories (CAT approximation)20 of 20
Rate categories were divided by 0.644 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 = -4084497.611 NNIs 1 max delta 0.00 Time 2152.76
Turning off heuristics for final round of ML NNIs (converged)
ML-NNI round 3: LogLk = -4084497.534 NNIs 0 max delta 0.00 Time 2481.43 (final)
Optimize all lengths: LogLk = -4084497.534 Time 2580.40
Terminado (killed)
but the newick file is empty!
I haven't had this problem before, I hope you can help me, please
Hi! I'm having problems with the generation of the newick file with FastTree, I wrote the next command:
FastTree -nt -gtr roaryresult/core_gene_alignment.aln > roaryresult/mytree.newick
and I have this answer:
FastTree Version 2.1.11 Double precision (No SSE3) Alignment: roaryresult/core_gene_alignment.aln 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 Initial topology in 24.29 secondshits for 1 of 34 seqs
Refining topology: 20 rounds ME-NNIs, 2 rounds ME-SPRs, 10 rounds ML-NNIs Total branch-length 0.067 after 279.50 sec 1 of 32 splits
ML-NNI round 1: LogLk = -4294141.116 NNIs 8 max delta 2413.17 Time 461.72 GTR Frequencies: 0.2964 0.1899 0.2146 0.2992ep 12 of 12
GTR rates(ac ag at cg ct gt) 1.1495 4.9822 0.9215 0.9770 7.1425 1.0000 Switched to using 20 rate categories (CAT approximation)20 of 20
Rate categories were divided by 0.644 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 = -4084497.611 NNIs 1 max delta 0.00 Time 2152.76 Turning off heuristics for final round of ML NNIs (converged) ML-NNI round 3: LogLk = -4084497.534 NNIs 0 max delta 0.00 Time 2481.43 (final) Optimize all lengths: LogLk = -4084497.534 Time 2580.40 Terminado (killed)
but the newick file is empty!
I haven't had this problem before, I hope you can help me, please
Dafne