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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 12-Jul-2021 18:21:04 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q494X3/2_msa/Q494X3_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q494X3/3_mltree/Q494X3.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q494X3/4_raxmlng_ancestral/Q494X3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626103264 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/Q494X3/2_msa/Q494X3_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 552 sites WARNING: Sequences tr_A0A2I2YQQ8_A0A2I2YQQ8_GORGO_9595 and sp_Q9Y2G7_ZFP30_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QM58_G3QM58_GORGO_9595 and tr_H2PSX1_H2PSX1_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QM58_G3QM58_GORGO_9595 and tr_H2R6I1_H2R6I1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QM58_G3QM58_GORGO_9595 and sp_O75820_ZN189_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QM58_G3QM58_GORGO_9595 and tr_A0A2R9AYB6_A0A2R9AYB6_PANPA_9597 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 tr_A0A2I3LH46_A0A2I3LH46_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2K6EBM5_A0A2K6EBM5_MACNE_9545 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_A0A2J8QIB0_A0A2J8QIB0_PANTR_9598 and sp_Q5MCW4_ZN569_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8QIH1_A0A2J8QIH1_PANTR_9598 and tr_A0A2R9AKC8_A0A2R9AKC8_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QG63_H2QG63_PANTR_9598 and sp_Q8N141_ZFP82_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QG63_H2QG63_PANTR_9598 and tr_A0A2R9AN39_A0A2R9AN39_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6UR85_F6UR85_MACMU_9544 and tr_A0A2K6ADH3_A0A2K6ADH3_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7DJD1_F7DJD1_MACMU_9544 and tr_G7PZ21_G7PZ21_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7DJD1_F7DJD1_MACMU_9544 and tr_A0A0A0MVX6_A0A0A0MVX6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DJD1_F7DJD1_MACMU_9544 and tr_A0A2K6CU82_A0A2K6CU82_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7F0N9_F7F0N9_MACMU_9544 and tr_A0A2K5LZF8_A0A2K5LZF8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7F0N9_F7F0N9_MACMU_9544 and tr_A0A2K6B2T5_A0A2K6B2T5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7F0N9_F7F0N9_MACMU_9544 and tr_A0A2K5YGT5_A0A2K5YGT5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7FTJ3_F7FTJ3_MACMU_9544 and tr_A0A2K6CFR0_A0A2K6CFR0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FX09_F7FX09_MACMU_9544 and tr_A0A2K6B732_A0A2K6B732_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GTJ8_F7GTJ8_MACMU_9544 and tr_A0A2K6BJH0_A0A2K6BJH0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HIL3_F7HIL3_MACMU_9544 and tr_A0A2K6D0A2_A0A2K6D0A2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HLX0_F7HLX0_MACMU_9544 and tr_A0A2K6AVH5_A0A2K6AVH5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HT77_F7HT77_MACMU_9544 and tr_A0A096P104_A0A096P104_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1L1C1_G1L1C1_AILME_9646 and tr_A0A384DGZ4_A0A384DGZ4_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7PRT6_G7PRT6_MACFA_9541 and tr_A0A2K5KKJ7_A0A2K5KKJ7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PRT6_G7PRT6_MACFA_9541 and tr_A0A2K5YQK9_A0A2K5YQK9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7PXE0_G7PXE0_MACFA_9541 and tr_A0A2K6D0J3_A0A2K6D0J3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0A0MVY8_A0A0A0MVY8_PAPAN_9555 and tr_A0A2K5YUH9_A0A2K5YUH9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0MW33_A0A0A0MW33_PAPAN_9555 and tr_A0A2K5ZEU7_A0A2K5ZEU7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5LAJ0_A0A2K5LAJ0_CERAT_9531 and tr_A0A2K5Y6G8_A0A2K5Y6G8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5N6M8_A0A2K5N6M8_CERAT_9531 and tr_A0A2K6BFV4_A0A2K6BFV4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5N6M8_A0A2K5N6M8_CERAT_9531 and tr_A0A2K6A534_A0A2K6A534_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4BTY2_A0A2U4BTY2_TURTR_9739 and tr_A0A2U4BU50_A0A2U4BU50_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4BUD3_A0A2U4BUD3_TURTR_9739 and tr_A0A2Y9P4L2_A0A2Y9P4L2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C4P0_A0A2U4C4P0_TURTR_9739 and tr_A0A2U4C4S2_A0A2U4C4S2_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4CGU5_A0A2U4CGU5_TURTR_9739 and tr_A0A2Y9QA60_A0A2Y9QA60_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CGU5_A0A2U4CGU5_TURTR_9739 and tr_A0A2Y9FJE6_A0A2Y9FJE6_PHYCD_9755 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/Q494X3/4_raxmlng_ancestral/Q494X3.raxml.reduced.phy Alignment comprises 1 partitions and 552 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 552 Gaps: 17.08 % Invariant sites: 0.72 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q494X3/4_raxmlng_ancestral/Q494X3.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/Q494X3/3_mltree/Q494X3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 138 / 11040 [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: -220407.655794 [00:00:00 -220407.655794] Initial branch length optimization [00:00:01 -219438.199409] Model parameter optimization (eps = 0.100000) [00:00:43] Tree #1, final logLikelihood: -219159.875924 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.134728,0.170247) (0.142273,0.541827) (0.346629,0.727337) (0.376369,1.721338) 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/Q494X3/4_raxmlng_ancestral/Q494X3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q494X3/4_raxmlng_ancestral/Q494X3.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q494X3/4_raxmlng_ancestral/Q494X3.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q494X3/4_raxmlng_ancestral/Q494X3.raxml.log Analysis started: 12-Jul-2021 18:21:04 / finished: 12-Jul-2021 18:21:53 Elapsed time: 48.870 seconds Consumed energy: 1.734 Wh