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 17:29:53 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31629/2_msa/P31629_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31629/3_mltree/P31629.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31629/4_raxmlng_ancestral/P31629 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100193 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/P31629/2_msa/P31629_nogap_msa.fasta [00:00:00] Loaded alignment with 959 taxa and 2446 sites WARNING: Sequences tr_M3XPF8_M3XPF8_MUSPF_9669 and tr_A0A2Y9KXL4_A0A2Y9KXL4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3R7D9_G3R7D9_GORGO_9595 and tr_A0A2J8Q1G0_A0A2J8Q1G0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R7D9_G3R7D9_GORGO_9595 and sp_Q9H2S9_IKZF4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R7D9_G3R7D9_GORGO_9595 and tr_A0A2R9CIJ3_A0A2R9CIJ3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_K7AFV7_K7AFV7_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_F7B8A3_F7B8A3_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_F6Q749_F6Q749_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_A0A096MW48_A0A096MW48_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_A0A2K5LBV8_A0A2K5LBV8_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_A0A2K6BT04_A0A2K6BT04_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_A0A2K5YC92_A0A2K5YC92_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_A0A2R9C8Y7_A0A2R9C8Y7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_A0A2U4BN70_A0A2U4BN70_TURTR_9739 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_A0A2Y9MW95_A0A2Y9MW95_DELLE_9749 are exactly identical! WARNING: Sequences tr_H2P8H4_H2P8H4_PONAB_9601 and tr_A0A384AKR0_A0A384AKR0_BALAS_310752 are exactly identical! WARNING: Sequences tr_J9NTQ0_J9NTQ0_CANLF_9615 and tr_M3WSR9_M3WSR9_FELCA_9685 are exactly identical! WARNING: Sequences tr_J9NTQ0_J9NTQ0_CANLF_9615 and tr_A0A2U3W197_A0A2U3W197_ODORO_9708 are exactly identical! WARNING: Sequences tr_J9NTQ0_J9NTQ0_CANLF_9615 and tr_A0A2U3XBG7_A0A2U3XBG7_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2I3SXN0_A0A2I3SXN0_PANTR_9598 and tr_A0A2R8ZPX2_A0A2R8ZPX2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QFA1_H2QFA1_PANTR_9598 and tr_A0A2R9BIL5_A0A2R9BIL5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R451_H2R451_PANTR_9598 and tr_A0A2R9A197_A0A2R9A197_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2RH32_H2RH32_PANTR_9598 and sp_Q96PQ6_ZN317_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2RH32_H2RH32_PANTR_9598 and tr_A0A2R9B2Z8_A0A2R9B2Z8_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7GJV4_F7GJV4_MACMU_9544 and tr_G7NUE6_G7NUE6_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7N7B0_G7N7B0_MACMU_9544 and tr_G7PIG3_G7PIG3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7N7B0_G7N7B0_MACMU_9544 and tr_A0A0D9QYY9_A0A0D9QYY9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7N7B0_G7N7B0_MACMU_9544 and tr_A0A2K5LTX4_A0A2K5LTX4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7N7B0_G7N7B0_MACMU_9544 and tr_A0A2K6AQT5_A0A2K6AQT5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7N7B0_G7N7B0_MACMU_9544 and tr_A0A2K5YE94_A0A2K5YE94_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7NNB5_G7NNB5_MACMU_9544 and tr_A0A096NPJ6_A0A096NPJ6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NNB5_G7NNB5_MACMU_9544 and tr_A0A0D9R5W8_A0A0D9R5W8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7NNB5_G7NNB5_MACMU_9544 and tr_A0A2K5MG20_A0A2K5MG20_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7NNB5_G7NNB5_MACMU_9544 and tr_A0A2K6B331_A0A2K6B331_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PZ22_G7PZ22_MACFA_9541 and tr_A0A2I3MEB8_A0A2I3MEB8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PZ22_G7PZ22_MACFA_9541 and tr_A0A2K5NZC2_A0A2K5NZC2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PZ22_G7PZ22_MACFA_9541 and tr_A0A2K6E8I7_A0A2K6E8I7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PZ49_G7PZ49_MACFA_9541 and tr_A0A2K5KVX6_A0A2K5KVX6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PZ49_G7PZ49_MACFA_9541 and tr_A0A2K5XT92_A0A2K5XT92_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2UG54_A0A2I2UG54_FELCA_9685 and tr_A0A2U3W090_A0A2U3W090_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A0V1PCE4_A0A0V1PCE4_9BILA_92180 and tr_A0A0V0U694_A0A0V0U694_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A2U3ZEB3_A0A2U3ZEB3_ODORO_9708 and tr_A0A2U3YA90_A0A2U3YA90_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/P31629/4_raxmlng_ancestral/P31629.raxml.reduced.phy Alignment comprises 1 partitions and 2446 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 2446 Gaps: 62.00 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31629/4_raxmlng_ancestral/P31629.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/P31629/3_mltree/P31629.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 612 / 48960 [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: -1547780.695534 [00:00:01 -1547780.695534] Initial branch length optimization [00:00:10 -766078.400120] Model parameter optimization (eps = 0.100000) [00:03:26] Tree #1, final logLikelihood: -755994.163535 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.201249,1.346602) (0.133418,1.771642) (0.190216,0.281786) (0.475117,0.924043) 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/P31629/4_raxmlng_ancestral/P31629.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31629/4_raxmlng_ancestral/P31629.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31629/4_raxmlng_ancestral/P31629.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P31629/4_raxmlng_ancestral/P31629.raxml.log Analysis started: 12-Jul-2021 17:29:53 / finished: 12-Jul-2021 17:33:42 Elapsed time: 228.869 seconds Consumed energy: 17.058 Wh