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-Jun-2021 15:29:50 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13224/2_msa/Q13224_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13224/3_mltree/Q13224.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13224/4_raxmlng_ancestral/Q13224 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622636990 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_020621/phylogeny-snakemake/results/Q13224/2_msa/Q13224_nogap_msa.fasta [00:00:00] Loaded alignment with 946 taxa and 1484 sites WARNING: Sequences tr_A0A2J8WWH6_A0A2J8WWH6_PONAB_9601 and sp_P42263_GRIA3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8WWH6_A0A2J8WWH6_PONAB_9601 and tr_A0A096N5U4_A0A096N5U4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2J8WWH6_A0A2J8WWH6_PONAB_9601 and tr_A0A2K6C368_A0A2K6C368_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2NGN9_H2NGN9_PONAB_9601 and sp_Q13224_NMDE2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1SD16_G1SD16_RABIT_9986 and tr_W5PVI2_W5PVI2_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1SD16_G1SD16_RABIT_9986 and tr_A0A2U4CHR8_A0A2U4CHR8_TURTR_9739 are exactly identical! WARNING: Sequences tr_G1SD16_G1SD16_RABIT_9986 and tr_A0A2Y9MEW1_A0A2Y9MEW1_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1SD16_G1SD16_RABIT_9986 and tr_A0A2Y9SYW0_A0A2Y9SYW0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2I3T979_A0A2I3T979_PANTR_9598 and tr_F7AGW3_F7AGW3_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3T979_A0A2I3T979_PANTR_9598 and tr_A0A2I3MXB9_A0A2I3MXB9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3T979_A0A2I3T979_PANTR_9598 and tr_A0A2K5M9E6_A0A2K5M9E6_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2Q5I0_H2Q5I0_PANTR_9598 and tr_A0A2R8ZSD1_A0A2R8ZSD1_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6T8S6_F6T8S6_MACMU_9544 and tr_G7PJX2_G7PJX2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6T8S6_F6T8S6_MACMU_9544 and tr_A0A2K6BQ06_A0A2K6BQ06_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6VTB5_F6VTB5_MACMU_9544 and tr_G7PRT2_G7PRT2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6VTB5_F6VTB5_MACMU_9544 and tr_A0A2K6DWU2_A0A2K6DWU2_MACNE_9545 are exactly identical! WARNING: Sequences tr_K7GKW9_K7GKW9_PIG_9823 and tr_A0A1U7TM63_A0A1U7TM63_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1M8E3_G1M8E3_AILME_9646 and tr_A0A2I2U7P0_A0A2I2U7P0_FELCA_9685 are exactly identical! WARNING: Sequences tr_G7Q3M1_G7Q3M1_MACFA_9541 and tr_A0A2K5MNX8_A0A2K5MNX8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7Q3M1_G7Q3M1_MACFA_9541 and tr_A0A2R8ZQ00_A0A2R8ZQ00_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A096NW97_A0A096NW97_PAPAN_9555 and tr_A0A2K5KMZ5_A0A2K5KMZ5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091J2D2_A0A091J2D2_EGRGA_188379 and tr_A0A091VMF1_A0A091VMF1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091J2D2_A0A091J2D2_EGRGA_188379 and tr_A0A087QUE3_A0A087QUE3_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JB59_A0A091JB59_EGRGA_188379 and tr_A0A091VM91_A0A091VM91_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JB59_A0A091JB59_EGRGA_188379 and tr_A0A0A0A7T4_A0A0A0A7T4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091W2J7_A0A091W2J7_NIPNI_128390 and tr_A0A087QLX8_A0A087QLX8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A226MJ56_A0A226MJ56_CALSU_9009 and tr_A0A226P6W1_A0A226P6W1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MYG0_A0A226MYG0_CALSU_9009 and tr_A0A226P0E8_A0A226P0E8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NFU6_A0A226NFU6_CALSU_9009 and tr_A0A226PEN6_A0A226PEN6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NGI4_A0A226NGI4_CALSU_9009 and tr_A0A226PL05_A0A226PL05_COLVI_9014 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_020621/phylogeny-snakemake/results/Q13224/4_raxmlng_ancestral/Q13224.raxml.reduced.phy Alignment comprises 1 partitions and 1484 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1484 Gaps: 45.86 % Invariant sites: 0.07 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13224/4_raxmlng_ancestral/Q13224.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_020621/phylogeny-snakemake/results/Q13224/3_mltree/Q13224.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 371 / 29680 [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: -498961.271081 [00:00:00 -498961.271081] Initial branch length optimization [00:00:12 -375308.117235] Model parameter optimization (eps = 0.100000) [00:02:26] Tree #1, final logLikelihood: -373612.788786 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.123654,0.316166) (0.093351,0.379601) (0.353359,0.614552) (0.429637,1.648629) 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_020621/phylogeny-snakemake/results/Q13224/4_raxmlng_ancestral/Q13224.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13224/4_raxmlng_ancestral/Q13224.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13224/4_raxmlng_ancestral/Q13224.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q13224/4_raxmlng_ancestral/Q13224.raxml.log Analysis started: 02-Jun-2021 15:29:50 / finished: 02-Jun-2021 15:32:30 Elapsed time: 159.062 seconds