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 02-Jun-2021 18:05:52 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IYU4/2_msa/Q8IYU4_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IYU4/3_mltree/Q8IYU4.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IYU4/4_raxmlng_ancestral/Q8IYU4 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622646352 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/020621_run/phylogeny-snakemake/results/Q8IYU4/2_msa/Q8IYU4_nogap_msa.fasta [00:00:00] Loaded alignment with 405 taxa and 475 sites WARNING: Sequences tr_M3XSF7_M3XSF7_MUSPF_9669 and tr_A0A2Y9K5I0_A0A2Y9K5I0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1S9B1_G1S9B1_NOMLE_61853 and tr_G3RLD1_G3RLD1_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S9B1_G1S9B1_NOMLE_61853 and sp_Q9UHD9_UBQL2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S9B1_G1S9B1_NOMLE_61853 and tr_A0A1D5QRK1_A0A1D5QRK1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S9B1_G1S9B1_NOMLE_61853 and tr_U3E4G7_U3E4G7_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1S9B1_G1S9B1_NOMLE_61853 and tr_G8F2K6_G8F2K6_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S9B1_G1S9B1_NOMLE_61853 and tr_A0A096N9W1_A0A096N9W1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S9B1_G1S9B1_NOMLE_61853 and tr_A0A0D9SAI4_A0A0D9SAI4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S9B1_G1S9B1_NOMLE_61853 and tr_A0A2K5NTM0_A0A2K5NTM0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S9B1_G1S9B1_NOMLE_61853 and tr_A0A2K6CXP7_A0A2K6CXP7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1S9B1_G1S9B1_NOMLE_61853 and tr_A0A2K5XVQ3_A0A2K5XVQ3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S9B1_G1S9B1_NOMLE_61853 and tr_A0A2R8ZET7_A0A2R8ZET7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2N5F3_H2N5F3_PONAB_9601 and tr_A0A2I3SFC5_A0A2I3SFC5_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2N5F3_H2N5F3_PONAB_9601 and tr_H2Q089_H2Q089_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2N5F3_H2N5F3_PONAB_9601 and sp_Q9NRR5_UBQL4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2N5F3_H2N5F3_PONAB_9601 and tr_A0A2R9BYX7_A0A2R9BYX7_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q5R684_UBQL1_PONAB_9601 and sp_Q9UMX0_UBQL1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5R684_UBQL1_PONAB_9601 and tr_A0A2R9BZC0_A0A2R9BZC0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G2HIQ5_G2HIQ5_PANTR_9598 and tr_A0A2R8ZML9_A0A2R8ZML9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A088A464_A0A088A464_APIME_7460 and tr_A0A2A3EM70_A0A2A3EM70_APICC_94128 are exactly identical! WARNING: Sequences tr_F6R260_F6R260_MACMU_9544 and tr_U3FE53_U3FE53_CALJA_9483 are exactly identical! WARNING: Sequences tr_F6R260_F6R260_MACMU_9544 and tr_A0A096NXU5_A0A096NXU5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6R260_F6R260_MACMU_9544 and tr_A0A2K5L544_A0A2K5L544_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6R260_F6R260_MACMU_9544 and tr_A0A2K6BAA2_A0A2K6BAA2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6R260_F6R260_MACMU_9544 and tr_A0A2K5ZCZ0_A0A2K5ZCZ0_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6ZTN5_F6ZTN5_MACMU_9544 and tr_A0A2K5KX40_A0A2K5KX40_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6ZTN5_F6ZTN5_MACMU_9544 and tr_A0A2K6B7W3_A0A2K6B7W3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NGE8_G7NGE8_MACMU_9544 and tr_A0A096P1V7_A0A096P1V7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NGE8_G7NGE8_MACMU_9544 and tr_A0A2K6DLW5_A0A2K6DLW5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NGE8_G7NGE8_MACMU_9544 and tr_A0A2K5XUX5_A0A2K5XUX5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3VA91_A0A2U3VA91_TURTR_9739 and tr_A0A2Y9MAV6_A0A2Y9MAV6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3VA91_A0A2U3VA91_TURTR_9739 and tr_A0A2Y9SA38_A0A2Y9SA38_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4BRR7_A0A2U4BRR7_TURTR_9739 and tr_A0A2Y9M0L6_A0A2Y9M0L6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BRR7_A0A2U4BRR7_TURTR_9739 and tr_A0A2Y9F4E2_A0A2Y9F4E2_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3WUV8_A0A2U3WUV8_ODORO_9708 and tr_A0A2Y9II03_A0A2Y9II03_ENHLU_391180 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/020621_run/phylogeny-snakemake/results/Q8IYU4/4_raxmlng_ancestral/Q8IYU4.raxml.reduced.phy Alignment comprises 1 partitions and 475 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 475 Gaps: 23.85 % Invariant sites: 0.21 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IYU4/4_raxmlng_ancestral/Q8IYU4.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/020621_run/phylogeny-snakemake/results/Q8IYU4/3_mltree/Q8IYU4.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 119 / 9520 [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: -63828.374897 [00:00:00 -63828.374897] Initial branch length optimization [00:00:00 -62521.082958] Model parameter optimization (eps = 0.100000) [00:00:27] Tree #1, final logLikelihood: -62168.604669 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.202647,1.514492) (0.076925,0.146039) (0.329226,0.440215) (0.391202,1.372510) 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/020621_run/phylogeny-snakemake/results/Q8IYU4/4_raxmlng_ancestral/Q8IYU4.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IYU4/4_raxmlng_ancestral/Q8IYU4.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IYU4/4_raxmlng_ancestral/Q8IYU4.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q8IYU4/4_raxmlng_ancestral/Q8IYU4.raxml.log Analysis started: 02-Jun-2021 18:05:52 / finished: 02-Jun-2021 18:06:21 Elapsed time: 29.261 seconds Consumed energy: 2.145 Wh