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 03-Jun-2021 02:25:03 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25189/2_msa/P25189_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25189/3_mltree/P25189.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25189/4_raxmlng_ancestral/P25189 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622676303 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/P25189/2_msa/P25189_nogap_msa.fasta [00:00:00] Loaded alignment with 508 taxa and 248 sites WARNING: Sequences tr_M3Y3E8_M3Y3E8_MUSPF_9669 and tr_F1PWS5_F1PWS5_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Y3E8_M3Y3E8_MUSPF_9669 and tr_A0A2Y9KHI6_A0A2Y9KHI6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1R704_G1R704_NOMLE_61853 and tr_G7PP32_G7PP32_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1R704_G1R704_NOMLE_61853 and tr_A0A096NXM1_A0A096NXM1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R704_G1R704_NOMLE_61853 and tr_A0A0D9S3K1_A0A0D9S3K1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R704_G1R704_NOMLE_61853 and tr_A0A2K5LCH1_A0A2K5LCH1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R704_G1R704_NOMLE_61853 and tr_A0A2K6DZ81_A0A2K6DZ81_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R704_G1R704_NOMLE_61853 and tr_A0A2K5ZTN6_A0A2K5ZTN6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QXH2_G3QXH2_GORGO_9595 and tr_A0A2J8X080_A0A2J8X080_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QXH2_G3QXH2_GORGO_9595 and tr_A0A2J8N1W1_A0A2J8N1W1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QXH2_G3QXH2_GORGO_9595 and sp_Q9NY72_SCN3B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QXH2_G3QXH2_GORGO_9595 and tr_F7I734_F7I734_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3QXH2_G3QXH2_GORGO_9595 and tr_A0A2R9AKY8_A0A2R9AKY8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RTC2_G3RTC2_GORGO_9595 and sp_O60487_MPZL2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RTC2_G3RTC2_GORGO_9595 and tr_A0A2R9ANP7_A0A2R9ANP7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8JAV0_A0A2J8JAV0_PANTR_9598 and tr_A0A2R9BG50_A0A2R9BG50_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R4A6_H2R4A6_PANTR_9598 and tr_A0A2R9AT83_A0A2R9AT83_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6Z4P8_F6Z4P8_HORSE_9796 and sp_Q6WEB5_MYP0_HORSE_9796 are exactly identical! WARNING: Sequences tr_W5NRA7_W5NRA7_SHEEP_9940 and sp_Q2KI11_SCN3B_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F7DA08_F7DA08_MACMU_9544 and tr_G7NXB1_G7NXB1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7DA08_F7DA08_MACMU_9544 and tr_A0A2K5M012_A0A2K5M012_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DA08_F7DA08_MACMU_9544 and tr_A0A2K6BFP4_A0A2K6BFP4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HDK6_F7HDK6_MACMU_9544 and tr_A0A2K6C1U7_A0A2K6C1U7_MACNE_9545 are exactly identical! WARNING: Sequences tr_H9YWR2_H9YWR2_MACMU_9544 and tr_A0A2K6DK65_A0A2K6DK65_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1M3I8_G1M3I8_AILME_9646 and tr_A0A384C063_A0A384C063_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7PPD3_G7PPD3_MACFA_9541 and tr_A0A096N6P0_A0A096N6P0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PPD3_G7PPD3_MACFA_9541 and tr_A0A0D9S446_A0A0D9S446_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7PPD3_G7PPD3_MACFA_9541 and tr_A0A2K6C0E8_A0A2K6C0E8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PPD3_G7PPD3_MACFA_9541 and tr_A0A2K5ZJZ4_A0A2K5ZJZ4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NCZ0_A0A096NCZ0_PAPAN_9555 and tr_A0A2K5LJG0_A0A2K5LJG0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NCZ0_A0A096NCZ0_PAPAN_9555 and tr_A0A2K5ZQ04_A0A2K5ZQ04_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091V975_A0A091V975_NIPNI_128390 and tr_A0A087QT15_A0A087QT15_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091V975_A0A091V975_NIPNI_128390 and tr_A0A0A0AW34_A0A0A0AW34_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A226MXW8_A0A226MXW8_CALSU_9009 and tr_A0A226P8T3_A0A226P8T3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U3V0X4_A0A2U3V0X4_TURTR_9739 and tr_A0A2Y9MCE9_A0A2Y9MCE9_DELLE_9749 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/P25189/4_raxmlng_ancestral/P25189.raxml.reduced.phy Alignment comprises 1 partitions and 248 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 248 Gaps: 19.89 % Invariant sites: 0.40 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25189/4_raxmlng_ancestral/P25189.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/P25189/3_mltree/P25189.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 62 / 4960 [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: -55819.217617 [00:00:00 -55819.217617] Initial branch length optimization [00:00:00 -52720.360625] Model parameter optimization (eps = 0.100000) [00:00:21] Tree #1, final logLikelihood: -52572.701128 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.099234,0.243700) (0.160582,0.474088) (0.454713,0.944610) (0.285471,1.646962) 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/P25189/4_raxmlng_ancestral/P25189.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25189/4_raxmlng_ancestral/P25189.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25189/4_raxmlng_ancestral/P25189.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25189/4_raxmlng_ancestral/P25189.raxml.log Analysis started: 03-Jun-2021 02:25:03 / finished: 03-Jun-2021 02:25:26 Elapsed time: 22.738 seconds Consumed energy: 1.469 Wh