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 12-Jul-2021 17:36:01 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/2_msa/A6NM62_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/3_mltree/A6NM62.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/4_raxmlng_ancestral/A6NM62 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100561 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/A6NM62/2_msa/A6NM62_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1247 sites WARNING: Sequences tr_M3Z502_M3Z502_MUSPF_9669 and tr_E2QXQ1_E2QXQ1_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z502_M3Z502_MUSPF_9669 and tr_A0A2I2UBS9_A0A2I2UBS9_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2I2ZDA6_A0A2I2ZDA6_GORGO_9595 and tr_A0A2I3RBH3_A0A2I3RBH3_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZDA6_A0A2I2ZDA6_GORGO_9595 and sp_Q86UN3_R4RL2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZSR1_A0A2I2ZSR1_GORGO_9595 and tr_H2NH22_H2NH22_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2ZSR1_A0A2I2ZSR1_GORGO_9595 and tr_H2Q5S1_H2Q5S1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZSR1_A0A2I2ZSR1_GORGO_9595 and sp_Q86SJ2_AMGO2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZSR1_A0A2I2ZSR1_GORGO_9595 and tr_A0A2R8ZJY3_A0A2R8ZJY3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SCU5_G3SCU5_GORGO_9595 and tr_H2R4I2_H2R4I2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SCU5_G3SCU5_GORGO_9595 and sp_Q8IW52_SLIK4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SCU5_G3SCU5_GORGO_9595 and tr_A0A2R8ZDQ2_A0A2R8ZDQ2_PANPA_9597 are exactly identical! WARNING: Sequences tr_F1PY08_F1PY08_CANLF_9615 and sp_Q5XM32_RXFP2_CANLF_9615 are exactly identical! WARNING: Sequences tr_F7FJR0_F7FJR0_MACMU_9544 and tr_G7PHN7_G7PHN7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FJR0_F7FJR0_MACMU_9544 and tr_A0A096NCW5_A0A096NCW5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FJR0_F7FJR0_MACMU_9544 and tr_A0A2K5L071_A0A2K5L071_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FJR0_F7FJR0_MACMU_9544 and tr_A0A2K6B1J7_A0A2K6B1J7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FJR0_F7FJR0_MACMU_9544 and tr_A0A2K5XI35_A0A2K5XI35_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HHZ1_F7HHZ1_MACMU_9544 and tr_G7PVK5_G7PVK5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HHZ1_F7HHZ1_MACMU_9544 and tr_A0A096N0C7_A0A096N0C7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HHZ1_F7HHZ1_MACMU_9544 and tr_A0A2K6CYS3_A0A2K6CYS3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PI19_G7PI19_MACFA_9541 and tr_A0A2K6E268_A0A2K6E268_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0A0MP87_A0A0A0MP87_BOVIN_9913 and sp_F1MLX5_LGR4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A096MW92_A0A096MW92_PAPAN_9555 and tr_A0A0D9SA21_A0A0D9SA21_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MW92_A0A096MW92_PAPAN_9555 and tr_A0A2K5NUP1_A0A2K5NUP1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MW92_A0A096MW92_PAPAN_9555 and tr_A0A2K6B2R1_A0A2K6B2R1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096MW92_A0A096MW92_PAPAN_9555 and tr_A0A2K5XYI5_A0A2K5XYI5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151N7P1_A0A151N7P1_ALLMI_8496 and tr_A0A1U7RS70_A0A1U7RS70_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0V1D5Q2_A0A0V1D5Q2_TRIBR_45882 and tr_A0A0V0TSJ8_A0A0V0TSJ8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A2U3WKC2_A0A2U3WKC2_ODORO_9708 and tr_A0A2U3XAX6_A0A2U3XAX6_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 29 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/A6NM62/4_raxmlng_ancestral/A6NM62.raxml.reduced.phy Alignment comprises 1 partitions and 1247 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1247 Gaps: 61.33 % Invariant sites: 0.08 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/4_raxmlng_ancestral/A6NM62.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/A6NM62/3_mltree/A6NM62.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 312 / 24960 [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: -381372.903799 [00:00:00 -381372.903799] Initial branch length optimization [00:00:02 -374918.847602] Model parameter optimization (eps = 0.100000) [00:01:22] Tree #1, final logLikelihood: -371766.790099 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.070582,0.348217) (0.059420,0.350935) (0.474544,1.027964) (0.395454,1.180304) 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/A6NM62/4_raxmlng_ancestral/A6NM62.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/4_raxmlng_ancestral/A6NM62.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/4_raxmlng_ancestral/A6NM62.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/4_raxmlng_ancestral/A6NM62.raxml.log Analysis started: 12-Jul-2021 17:36:01 / finished: 12-Jul-2021 17:37:34 Elapsed time: 93.492 seconds Consumed energy: 7.079 Wh