IQ-TREE multicore version 1.6.10 for Windows 64-bit built Feb 19 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: cardenas (AVX2, FMA3, 15 GB RAM) Command: D:\Graduate School\Trachy manuscript\GENOME_delimitation\IQ_tree\bin\iqtree.exe -s concatenated_samples.nex -o Myc_tur_571_CR071225_02 -spp parti.nex -m MF+MERGE Seed: 807162 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Tue Oct 08 10:25:55 2019 Kernel: AVX+FMA - 1 threads (12 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 12 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading partition model file parti.nex ... Reading alignment file concatenated_samples.nex ... Nexus format detected Skipping unknown block (SETS)... Alignment has 11 sequences with 2749 columns, 64 distinct patterns 25 parsimony-informative, 50 singleton sites, 2674 constant sites Gap/Ambiguity Composition p-value 1 Myc_nsp_312_UGM951118_02 11.09% passed 98.74% 2 Myc_nsp_449_RMMA050801_08 0.00% passed 99.92% 3 Myc_nsp_450_RMMA050727_06 0.00% passed 100.00% 4 Myc_nsp_575_JSC030826_01 0.00% passed 99.93% 5 Myc_nsp_858_RMMA090930_09 0.00% passed 99.93% 6 Myc_nsp_862_RMMA050105_29 0.00% passed 99.93% 7 Myc_zet_451_RMMA050816_04 0.00% passed 99.64% 8 Myc_zet_A444_RMMA050818_05 2.18% passed 98.90% 9 Myc_tur_571_CR071225_02 0.04% passed 99.95% 10 Myc_tur_T25_CR051012_01 15.13% passed 88.73% 11 Tzet1.0 0.00% passed 99.93% **** TOTAL 2.59% 0 sequences failed composition chi2 test (p-value<5%; df=3) NOTE: No CharPartition defined, use all CharSets Loading 4 partitions... Subset Type Seqs Sites Infor Invar Model Name 1 11 1074 12 1035 MF+MERGE genome_F1 2 11 516 2 510 MF+MERGE genome_F2 3 11 456 4 450 MF+MERGE genome_LWRh 4 11 703 7 679 MF+MERGE genome_WG Degree of missing data: 0.000 Info: multi-threading strategy over partitions NOTE: Myc_nsp_858_RMMA090930_09 is identical to Myc_nsp_575_JSC030826_01 but kept for subsequent analysis NOTE: 2 identical sequences (see below) will be ignored for subsequent analysis NOTE: Myc_nsp_862_RMMA050105_29 (identical to Myc_nsp_575_JSC030826_01) is ignored but added at the end NOTE: Tzet1.0 (identical to Myc_nsp_575_JSC030826_01) is ignored but added at the end Concatenated alignment was printed to parti.nex.uniqueseq.phy For your convenience alignment with unique sequences printed to parti.nex.uniqueseq.phy Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.005 seconds NOTE: ModelFinder requires 0 MB RAM! Testing GTR+F+G on supermatrix... GTR+F+G4 / LnL: -4358.692 / df: 24 / AIC: 8765.384 / AICc: 8765.824 / BIC: 8907.439 Selecting individual models for 4 charsets using BIC... No. Model Score Charset 1 K2P+I 3568.550 genome_F1 2 JC 1543.452 genome_F2 3 K2P 1362.542 genome_LWRh 4 K2P 2288.251 genome_WG Full partition model BIC score: 8884.474 (LnL: -4355.128 df:22) Merging models to increase model fit (about 13 total partition schemes)... 5 K2P+I 8884.863 genome_F1+genome_F2 6 K3P+I 8887.749 genome_F1+genome_LWRh 7 K2P+I 8871.821 genome_F1+genome_WG 8 K2P 8876.708 genome_F2+genome_LWRh 9 K2P 8883.818 genome_F2+genome_WG 10 K2P 8876.739 genome_LWRh+genome_WG 0h:0m:1s (0h:0m:0s left) Merging genome_F1+genome_WG with BIC score: 8871.821 (LnL: -4356.720 df: 20) 11 K2P+I 8873.498 genome_F1+genome_F2+genome_WG 0h:0m:1s (0h:0m:0s left) 12 TNe+I 8874.620 genome_F1+genome_LWRh+genome_WG 0h:0m:1s (0h:0m:0s left) Merging genome_F2+genome_LWRh with BIC score: 8864.055 (LnL: -4356.797 df: 19) 13 K2P+I 8866.344 genome_F1+genome_F2+genome_LWRh+genome_WG 0h:0m:1s (0h:0m:0s left) BEST-FIT PARTITION MODEL: charpartition BIC = K2P+I: genome_F1 genome_WG, K2P: genome_F2 genome_LWRh; Agglomerative model selection: ((genome_F1,genome_WG)1:8871.82,(genome_F2,genome_LWRh)2:8864.06) Merging into 2 partitions... Partition information was printed to parti.nex.best_scheme.nex Partition information in Raxml format was printed to parti.nex.best_scheme All model information printed to parti.nex.model.gz CPU time for ModelFinder: 1.719 seconds (0h:0m:1s) Wall-clock time for ModelFinder: 1.971 seconds (0h:0m:1s) NOTE: 0 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.010) Initial log-likelihood: -4404.417 Current log-likelihood at step 1: -4364.245 Current log-likelihood at step 2: -4364.036 Current log-likelihood at step 3: -4363.936 Current log-likelihood at step 4: -4363.840 Current log-likelihood at step 5: -4363.743 Current log-likelihood at step 6: -4363.644 Current log-likelihood at step 7: -4363.545 Current log-likelihood at step 8: -4363.445 Current log-likelihood at step 9: -4363.343 Current log-likelihood at step 10: -4363.241 Current log-likelihood at step 11: -4363.137 Current log-likelihood at step 12: -4363.032 Current log-likelihood at step 13: -4362.926 Current log-likelihood at step 14: -4362.818 Current log-likelihood at step 15: -4362.710 Current log-likelihood at step 16: -4362.600 Current log-likelihood at step 17: -4362.489 Current log-likelihood at step 18: -4362.376 Current log-likelihood at step 19: -4362.262 Current log-likelihood at step 20: -4362.147 Current log-likelihood at step 21: -4362.030 Current log-likelihood at step 22: -4361.913 Current log-likelihood at step 23: -4361.793 Current log-likelihood at step 24: -4361.673 Current log-likelihood at step 25: -4361.551 Current log-likelihood at step 26: -4361.428 Current log-likelihood at step 27: -4361.303 Current log-likelihood at step 28: -4361.177 Current log-likelihood at step 29: -4361.050 Current log-likelihood at step 30: -4360.922 Current log-likelihood at step 31: -4360.792 Current log-likelihood at step 32: -4360.661 Current log-likelihood at step 33: -4360.529 Current log-likelihood at step 34: -4360.396 Current log-likelihood at step 35: -4360.262 Current log-likelihood at step 36: -4360.127 Current log-likelihood at step 37: -4359.991 Current log-likelihood at step 38: -4359.854 Current log-likelihood at step 39: -4359.716 Current log-likelihood at step 40: -4359.579 Current log-likelihood at step 41: -4359.440 Current log-likelihood at step 42: -4356.717 Current log-likelihood at step 43: -4356.711 Partition-specific rates: 1.340 0.378 Parameters optimization took 42 rounds (0.120 sec) BEST SCORE FOUND : -4356.711 Total tree length: 0.033 Total number of iterations: 0 CPU time used for tree search: 0.000 sec (0h:0m:0s) Wall-clock time used for tree search: 0.000 sec (0h:0m:0s) Total CPU time used: 0.047 sec (0h:0m:0s) Total wall-clock time used: 0.148 sec (0h:0m:0s) Analysis results written to: IQ-TREE report: parti.nex.iqtree Tree used for ModelFinder: parti.nex.treefile Best partitioning scheme: parti.nex.best_scheme.nex in RAxML format: parti.nex.best_scheme Screen log file: parti.nex.log Date and Time: Tue Oct 08 10:25:58 2019