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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 12-Jul-2021 17:25:07 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/2_msa/Q3SXY7_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/3_mltree/Q3SXY7.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/4_raxmlng_ancestral/Q3SXY7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099907 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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/2_msa/Q3SXY7_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 679 sites WARNING: Sequences sp_P0C192_LRC4B_MOUSE_10090 and sp_P0CC10_LRC4B_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Z8E8_M3Z8E8_MUSPF_9669 and tr_A0A2Y9JQM1_A0A2Y9JQM1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1R366_G1R366_NOMLE_61853 and tr_A0A096N284_A0A096N284_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R366_G1R366_NOMLE_61853 and tr_A0A2K5L840_A0A2K5L840_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R366_G1R366_NOMLE_61853 and tr_A0A2K6D887_A0A2K6D887_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3SJH4_G3SJH4_GORGO_9595 and sp_Q9BXN1_ASPN_HUMAN_9606 are exactly identical! WARNING: Sequences tr_C3ZS65_C3ZS65_BRAFL_7739 and tr_C3ZS67_C3ZS67_BRAFL_7739 are exactly identical! WARNING: Sequences tr_E2RH90_E2RH90_CANLF_9615 and tr_D2GWR2_D2GWR2_AILME_9646 are exactly identical! WARNING: Sequences tr_E2RH90_E2RH90_CANLF_9615 and tr_A0A2U3YUV5_A0A2U3YUV5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_E2RH90_E2RH90_CANLF_9615 and tr_A0A384DAI9_A0A384DAI9_URSMA_29073 are exactly identical! WARNING: Sequences tr_H2Q8Q8_H2Q8Q8_PANTR_9598 and tr_A0A2R8Z827_A0A2R8Z827_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QGY2_H2QGY2_PANTR_9598 and sp_Q9NT99_LRC4B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QVB4_H2QVB4_PANTR_9598 and tr_A0A2R9A6Z7_A0A2R9A6Z7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R7M6_H2R7M6_PANTR_9598 and tr_A0A2R9A5N3_A0A2R9A5N3_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7D2Z3_K7D2Z3_PANTR_9598 and sp_Q6PJG9_LRFN4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7D2Z3_K7D2Z3_PANTR_9598 and tr_A0A2R9A0Z5_A0A2R9A0Z5_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7D663_K7D663_PANTR_9598 and tr_A0A2K6DJA2_A0A2K6DJA2_MACNE_9545 are exactly identical! WARNING: Sequences tr_M4AYQ2_M4AYQ2_XIPMA_8083 and tr_A0A087YRR4_A0A087YRR4_POEFO_48698 are exactly identical! WARNING: Sequences tr_F6Q3P7_F6Q3P7_MACMU_9544 and tr_A0A0D9SCQ8_A0A0D9SCQ8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6WZ84_F6WZ84_MACMU_9544 and tr_G7PEW5_G7PEW5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WZ84_F6WZ84_MACMU_9544 and tr_A0A2K6BRT8_A0A2K6BRT8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6YJL6_F6YJL6_MACMU_9544 and tr_A0A2K6AXI0_A0A2K6AXI0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BEN4_F7BEN4_MACMU_9544 and tr_G7PB44_G7PB44_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7BEN4_F7BEN4_MACMU_9544 and tr_A0A2K6AU17_A0A2K6AU17_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0YW98_H0YW98_TAEGU_59729 and tr_A0A091ENY6_A0A091ENY6_CORBR_85066 are exactly identical! WARNING: Sequences tr_G7PI19_G7PI19_MACFA_9541 and tr_A0A096MVL6_A0A096MVL6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PI19_G7PI19_MACFA_9541 and tr_A0A2K6E268_A0A2K6E268_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PI19_G7PI19_MACFA_9541 and tr_A0A2K5Y3N5_A0A2K5Y3N5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0MP87_A0A0A0MP87_BOVIN_9913 and sp_F1MLX5_LGR4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A096NB36_A0A096NB36_PAPAN_9555 and tr_A0A2K6CU43_A0A2K6CU43_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NDZ4_A0A096NDZ4_PAPAN_9555 and tr_A0A0D9SCU5_A0A0D9SCU5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NDZ4_A0A096NDZ4_PAPAN_9555 and tr_A0A2K5XU37_A0A2K5XU37_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0MVU1_A0A0A0MVU1_PAPAN_9555 and tr_A0A2K5KY06_A0A2K5KY06_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0A0MVU1_A0A0A0MVU1_PAPAN_9555 and tr_A0A2K5XDC3_A0A2K5XDC3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151N6V5_A0A151N6V5_ALLMI_8496 and tr_A0A1U7R1D4_A0A1U7R1D4_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NLG0_A0A151NLG0_ALLMI_8496 and tr_A0A1U7SFS0_A0A1U7SFS0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A2D0PXC6_A0A2D0PXC6_ICTPU_7998 and tr_A0A2D0Q1B1_A0A2D0Q1B1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PXD1_A0A2D0PXD1_ICTPU_7998 and tr_A0A2D0PYP6_A0A2D0PYP6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PXD1_A0A2D0PXD1_ICTPU_7998 and tr_A0A2D0Q0D9_A0A2D0Q0D9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3UZJ5_A0A2U3UZJ5_TURTR_9739 and tr_A0A383ZQ82_A0A383ZQ82_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3WIV2_A0A2U3WIV2_ODORO_9708 and tr_A0A2U3X7C0_A0A2U3X7C0_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 41 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/4_raxmlng_ancestral/Q3SXY7.raxml.reduced.phy Alignment comprises 1 partitions and 679 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 679 Gaps: 39.61 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/4_raxmlng_ancestral/Q3SXY7.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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/3_mltree/Q3SXY7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 170 / 13600 [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: -247220.443548 [00:00:00 -247220.443548] Initial branch length optimization [00:00:01 -244192.385177] Model parameter optimization (eps = 0.100000) [00:01:06] Tree #1, final logLikelihood: -243041.928755 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.082695,0.370138) (0.075639,0.398074) (0.405863,0.877834) (0.435803,1.337764) 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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/4_raxmlng_ancestral/Q3SXY7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/4_raxmlng_ancestral/Q3SXY7.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/4_raxmlng_ancestral/Q3SXY7.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/4_raxmlng_ancestral/Q3SXY7.raxml.log Analysis started: 12-Jul-2021 17:25:07 / finished: 12-Jul-2021 17:26:20 Elapsed time: 72.413 seconds Consumed energy: 6.094 Wh