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 17:54:37 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L2E3/2_msa/Q7L2E3_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L2E3/3_mltree/Q7L2E3.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L2E3/4_raxmlng_ancestral/Q7L2E3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101677 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/Q7L2E3/2_msa/Q7L2E3_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1194 sites WARNING: Sequences tr_G1S8P5_G1S8P5_NOMLE_61853 and tr_G3SFU0_G3SFU0_GORGO_9595 are exactly identical! WARNING: Sequences tr_B2WNJ0_B2WNJ0_PYRTR_426418 and tr_A0A2W1E7Q6_A0A2W1E7Q6_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3SKQ4_G3SKQ4_GORGO_9595 and tr_H2QNM0_H2QNM0_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q5R874_DHX9_PONAB_9601 and tr_H2Q0R0_H2Q0R0_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q5R874_DHX9_PONAB_9601 and sp_Q08211_DHX9_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5R874_DHX9_PONAB_9601 and tr_F6W5Y4_F6W5Y4_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q5R874_DHX9_PONAB_9601 and tr_A0A2K6DJY7_A0A2K6DJY7_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q5R874_DHX9_PONAB_9601 and tr_A0A2R9AB38_A0A2R9AB38_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0FFG1_A0A0E0FFG1_ORYNI_4536 and tr_A0A0E0MQN3_A0A0E0MQN3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GTP4_A0A0E0GTP4_ORYNI_4536 and tr_B8AJW1_B8AJW1_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GTP4_A0A0E0GTP4_ORYNI_4536 and tr_A0A0E0P1B3_A0A0E0P1B3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GTP4_A0A0E0GTP4_ORYNI_4536 and tr_A0A0P0W309_A0A0P0W309_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F7D9X5_F7D9X5_MACMU_9544 and tr_A0A2K6B4G5_A0A2K6B4G5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A2XTL2_A2XTL2_ORYSI_39946 and tr_I1PLD7_I1PLD7_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2XTL2_A2XTL2_ORYSI_39946 and tr_A0A0D3FW09_A0A0D3FW09_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_G7NZL0_G7NZL0_MACFA_9541 and tr_A0A096N6F2_A0A096N6F2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NZL0_G7NZL0_MACFA_9541 and tr_A0A2K6DAR7_A0A2K6DAR7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NZL0_G7NZL0_MACFA_9541 and tr_A0A2K5YP21_A0A2K5YP21_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5E5N3_G5E5N3_BOVIN_9913 and sp_Q28141_DHX9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A067FI17_A0A067FI17_CITSI_2711 and tr_V4UR24_V4UR24_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A096NWR7_A0A096NWR7_PAPAN_9555 and tr_A0A2K5L8V6_A0A2K5L8V6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NWR7_A0A096NWR7_PAPAN_9555 and tr_A0A2K5ZUW5_A0A2K5ZUW5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A078J242_A0A078J242_BRANA_3708 and tr_A0A0D3D9Z7_A0A0D3D9Z7_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0A1ML61_A0A0A1ML61_9FUNG_58291 and tr_A0A367KCK6_A0A367KCK6_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A087QJJ0_A0A087QJJ0_APTFO_9233 and tr_A0A091G9X6_A0A091G9X6_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1S3YXD1_A0A1S3YXD1_TOBAC_4097 and tr_A0A1U7VQK7_A0A1U7VQK7_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4BDM1_A0A1S4BDM1_TOBAC_4097 and tr_A0A1J6IXT6_A0A1J6IXT6_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S4BDM1_A0A1S4BDM1_TOBAC_4097 and tr_A0A1U7YEG9_A0A1U7YEG9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CT96_A0A1S4CT96_TOBAC_4097 and tr_A0A1U7XFG9_A0A1U7XFG9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2D0RAW5_A0A2D0RAW5_ICTPU_7998 and tr_A0A2D0RCT6_A0A2D0RCT6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3V155_A0A2U3V155_TURTR_9739 and tr_A0A2U4C9W9_A0A2U4C9W9_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U3V1F3_A0A2U3V1F3_TURTR_9739 and tr_A0A2U4CA58_A0A2U4CA58_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U3V1Q8_A0A2U3V1Q8_TURTR_9739 and tr_A0A2U4C9W8_A0A2U4C9W8_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4C9V9_A0A2U4C9V9_TURTR_9739 and tr_A0A2U4C9X2_A0A2U4C9X2_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U3VP84_A0A2U3VP84_ODORO_9708 and tr_A0A2U3XD06_A0A2U3XD06_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 35 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/Q7L2E3/4_raxmlng_ancestral/Q7L2E3.raxml.reduced.phy Alignment comprises 1 partitions and 1194 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1194 Gaps: 26.59 % Invariant sites: 0.75 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L2E3/4_raxmlng_ancestral/Q7L2E3.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/Q7L2E3/3_mltree/Q7L2E3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 299 / 23920 [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: -465153.692773 [00:00:00 -465153.692773] Initial branch length optimization [00:00:02 -461213.570417] Model parameter optimization (eps = 0.100000) [00:00:49] Tree #1, final logLikelihood: -460341.765836 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.126840,0.195077) (0.184352,0.295385) (0.314095,0.815995) (0.374713,1.773361) 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/Q7L2E3/4_raxmlng_ancestral/Q7L2E3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L2E3/4_raxmlng_ancestral/Q7L2E3.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L2E3/4_raxmlng_ancestral/Q7L2E3.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L2E3/4_raxmlng_ancestral/Q7L2E3.raxml.log Analysis started: 12-Jul-2021 17:54:37 / finished: 12-Jul-2021 17:55:38 Elapsed time: 60.298 seconds Consumed energy: 4.746 Wh