RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 02-Aug-2021 21:57:33 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5EBL2/2_msa/Q5EBL2_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5EBL2/3_mltree/Q5EBL2.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5EBL2/4_raxmlng_ancestral/Q5EBL2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1627930653 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5EBL2/2_msa/Q5EBL2_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1059 sites WARNING: Sequences tr_A0A2I2YYI0_A0A2I2YYI0_GORGO_9595 and tr_K7EU23_K7EU23_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2YYI0_A0A2I2YYI0_GORGO_9595 and tr_H2QG67_H2QG67_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YYI0_A0A2I2YYI0_GORGO_9595 and tr_A0A2K5NSA5_A0A2K5NSA5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2I3T1I2_A0A2I3T1I2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and sp_Q99676_ZN184_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2K5XY05_A0A2K5XY05_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2R9C8X5_A0A2R9C8X5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8U9W7_A0A2J8U9W7_PONAB_9601 and tr_F6PVJ2_F6PVJ2_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2J8U9W7_A0A2J8U9W7_PONAB_9601 and tr_A0A2K6E5U8_A0A2K6E5U8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2J8Q707_A0A2J8Q707_PANTR_9598 and sp_Q6ZN19_ZN841_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8Q7D1_A0A2J8Q7D1_PANTR_9598 and sp_Q9HCG1_ZN160_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R535_H2R535_PANTR_9598 and tr_A0A2R9C791_A0A2R9C791_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QC17_A0A1D5QC17_MACMU_9544 and tr_A0A2K6BUH3_A0A2K6BUH3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QCB8_A0A1D5QCB8_MACMU_9544 and tr_G7P743_G7P743_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QCB8_A0A1D5QCB8_MACMU_9544 and tr_A0A096N6B2_A0A096N6B2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QCB8_A0A1D5QCB8_MACMU_9544 and tr_A0A2K6AWJ5_A0A2K6AWJ5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QCB8_A0A1D5QCB8_MACMU_9544 and tr_A0A2K5XH95_A0A2K5XH95_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6WPD0_F6WPD0_MACMU_9544 and tr_A0A096P278_A0A096P278_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6ZAL5_F6ZAL5_MACMU_9544 and tr_G7PXE1_G7PXE1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6ZAL5_F6ZAL5_MACMU_9544 and tr_A0A2K6ALM5_A0A2K6ALM5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GLK7_F7GLK7_MACMU_9544 and tr_A0A2K6DH52_A0A2K6DH52_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GLK7_F7GLK7_MACMU_9544 and tr_A0A2K5Y2N5_A0A2K5Y2N5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1MIT5_G1MIT5_AILME_9646 and tr_A0A2U3ZBT1_A0A2U3ZBT1_ODORO_9708 are exactly identical! WARNING: Sequences sp_A2VDQ7_ZN420_BOVIN_9913 and tr_F1MML9_F1MML9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A2I3LH46_A0A2I3LH46_PAPAN_9555 and tr_A0A0D9R6H9_A0A0D9R6H9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2K5LMS6_A0A2K5LMS6_CERAT_9531 and tr_A0A2K5YZS4_A0A2K5YZS4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4C4P0_A0A2U4C4P0_TURTR_9739 and tr_A0A2U4C4S2_A0A2U4C4S2_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4C4P0_A0A2U4C4P0_TURTR_9739 and tr_A0A2Y9M7X8_A0A2Y9M7X8_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CMQ1_A0A2U4CMQ1_TURTR_9739 and tr_A0A2Y9EF59_A0A2Y9EF59_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4CMQ1_A0A2U4CMQ1_TURTR_9739 and tr_A0A383ZFA2_A0A383ZFA2_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 30 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5EBL2/4_raxmlng_ancestral/Q5EBL2.raxml.reduced.phy Alignment comprises 1 partitions and 1059 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1059 Gaps: 47.67 % Invariant sites: 0.47 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5EBL2/4_raxmlng_ancestral/Q5EBL2.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5EBL2/3_mltree/Q5EBL2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 265 / 21200 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:00] Tree #1, initial LogLikelihood: -374660.301794 [00:00:00 -374660.301794] Initial branch length optimization [00:00:02 -371401.597781] Model parameter optimization (eps = 0.100000) [00:00:59] Tree #1, final logLikelihood: -370600.974071 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.112363,0.155566) (0.068738,0.269981) (0.354961,0.576539) (0.463938,1.636670) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Marginal ancestral probabilities saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5EBL2/4_raxmlng_ancestral/Q5EBL2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5EBL2/4_raxmlng_ancestral/Q5EBL2.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5EBL2/4_raxmlng_ancestral/Q5EBL2.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5EBL2/4_raxmlng_ancestral/Q5EBL2.raxml.log Analysis started: 02-Aug-2021 21:57:33 / finished: 02-Aug-2021 21:58:41 Elapsed time: 68.586 seconds