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 03-Jun-2021 02:45:26 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51681/2_msa/P51681_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51681/3_mltree/P51681.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51681/4_raxmlng_ancestral/P51681 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677526 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/P51681/2_msa/P51681_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 352 sites WARNING: Sequences tr_A0A2I3H6V3_A0A2I3H6V3_NOMLE_61853 and tr_A0A2I3TX94_A0A2I3TX94_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R2I4_G1R2I4_NOMLE_61853 and tr_G3S0Y6_G3S0Y6_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R2I4_G1R2I4_NOMLE_61853 and tr_H2R8C2_H2R8C2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RC17_G3RC17_GORGO_9595 and tr_H2QM91_H2QM91_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RC17_G3RC17_GORGO_9595 and sp_P51679_CCR4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RC17_G3RC17_GORGO_9595 and tr_A0A2R8ZA62_A0A2R8ZA62_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RJP4_G3RJP4_GORGO_9595 and tr_H2NU74_H2NU74_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RJP4_G3RJP4_GORGO_9595 and tr_H2R9P0_H2R9P0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RJP4_G3RJP4_GORGO_9595 and sp_P32248_CCR7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RJP4_G3RJP4_GORGO_9595 and tr_A0A2R9CE39_A0A2R9CE39_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1U5C9_G1U5C9_RABIT_9986 and sp_Q2KTE1_CX3C1_RABIT_9986 are exactly identical! WARNING: Sequences tr_G1K2B4_G1K2B4_CANLF_9615 and sp_Q64H34_CCR3_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3SLL0_A0A2I3SLL0_PANTR_9598 and tr_A0A2R8ZPK3_A0A2R8ZPK3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2RCA7_H2RCA7_PANTR_9598 and tr_A0A2R9AZT7_A0A2R9AZT7_PANPA_9597 are exactly identical! WARNING: Sequences sp_P56440_CCR5_PANTR_9598 and sp_P60574_CCR5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QNH5_A0A1D5QNH5_MACMU_9544 and sp_P61813_CCR5_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A1D5QNH5_A0A1D5QNH5_MACMU_9544 and tr_G7NY33_G7NY33_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QNH5_A0A1D5QNH5_MACMU_9544 and tr_A0A2K6BMC9_A0A2K6BMC9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QNH5_A0A1D5QNH5_MACMU_9544 and sp_P61815_CCR5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6QJR2_F6QJR2_MACMU_9544 and tr_G7NY36_G7NY36_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6U6G8_F6U6G8_MACMU_9544 and tr_G7NYJ2_G7NYJ2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6VQA9_F6VQA9_MACMU_9544 and tr_G7P491_G7P491_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WHR2_F6WHR2_MACMU_9544 and tr_G7PUP1_G7PUP1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WHR2_F6WHR2_MACMU_9544 and tr_A0A2I3LW21_A0A2I3LW21_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WHR2_F6WHR2_MACMU_9544 and tr_A0A0D9S306_A0A0D9S306_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6WHR2_F6WHR2_MACMU_9544 and tr_A0A2K5YEY1_A0A2K5YEY1_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GUA3_F7GUA3_MACMU_9544 and tr_G7NYB7_G7NYB7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GUA3_F7GUA3_MACMU_9544 and tr_A0A096NRU6_A0A096NRU6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GUA3_F7GUA3_MACMU_9544 and tr_A0A0D9SC57_A0A0D9SC57_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GUA3_F7GUA3_MACMU_9544 and tr_G9IT94_G9IT94_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GUA3_F7GUA3_MACMU_9544 and tr_A0A2K6AVR0_A0A2K6AVR0_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0Z1W0_H0Z1W0_TAEGU_59729 and tr_H1A526_H1A526_TAEGU_59729 are exactly identical! WARNING: Sequences tr_G7NY39_G7NY39_MACFA_9541 and tr_A0A096NQ44_A0A096NQ44_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NY39_G7NY39_MACFA_9541 and tr_A0A2K5NXR5_A0A2K5NXR5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7NY39_G7NY39_MACFA_9541 and tr_A0A2K6BC31_A0A2K6BC31_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NY39_G7NY39_MACFA_9541 and tr_A0A2K6AAY8_A0A2K6AAY8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A226MAR3_A0A226MAR3_CALSU_9009 and tr_A0A226MC70_A0A226MC70_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A2D0RJV6_A0A2D0RJV6_ICTPU_7998 and tr_A0A2D0RJW6_A0A2D0RJW6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RQH5_A0A2D0RQH5_ICTPU_7998 and tr_A0A2D0RQJ1_A0A2D0RQJ1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RQH5_A0A2D0RQH5_ICTPU_7998 and tr_A0A2D0RS37_A0A2D0RS37_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KRT5_A0A2K5KRT5_CERAT_9531 and tr_A0A2K5ZZK3_A0A2K5ZZK3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5KT08_A0A2K5KT08_CERAT_9531 and tr_A0A2K5XW18_A0A2K5XW18_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 42 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/P51681/4_raxmlng_ancestral/P51681.raxml.reduced.phy Alignment comprises 1 partitions and 352 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 352 Gaps: 8.07 % Invariant sites: 0.28 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51681/4_raxmlng_ancestral/P51681.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/P51681/3_mltree/P51681.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 88 / 7040 [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: -173118.421504 [00:00:00 -173118.421504] Initial branch length optimization [00:00:00 -172941.904088] Model parameter optimization (eps = 0.100000) [00:00:24] Tree #1, final logLikelihood: -172493.943721 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.184536,0.362309) (0.241038,0.486711) (0.426497,1.105495) (0.147929,2.327705) 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/P51681/4_raxmlng_ancestral/P51681.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51681/4_raxmlng_ancestral/P51681.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51681/4_raxmlng_ancestral/P51681.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P51681/4_raxmlng_ancestral/P51681.raxml.log Analysis started: 03-Jun-2021 02:45:26 / finished: 03-Jun-2021 02:45:54 Elapsed time: 27.409 seconds Consumed energy: 2.060 Wh