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 02:34:27 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15746/2_msa/Q15746_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15746/3_mltree/Q15746.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15746/4_raxmlng_ancestral/Q15746 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622676867 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/Q15746/2_msa/Q15746_nogap_msa.fasta [00:00:00] Loaded alignment with 997 taxa and 1914 sites WARNING: Sequences sp_O54784_DAPK3_MOUSE_10090 and sp_O88764_DAPK3_RAT_10116 are exactly identical! WARNING: Sequences tr_G1QZR2_G1QZR2_NOMLE_61853 and tr_H2R0V4_H2R0V4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QZR2_G1QZR2_NOMLE_61853 and sp_P53355_DAPK1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QZR2_G1QZR2_NOMLE_61853 and tr_A0A2K5M5T8_A0A2K5M5T8_CERAT_9531 are exactly identical! WARNING: Sequences tr_E2QVH6_E2QVH6_CANLF_9615 and tr_A0A2U3VKF3_A0A2U3VKF3_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2QVH6_E2QVH6_CANLF_9615 and tr_A0A2U3Y4Y3_A0A2U3Y4Y3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_E2QVH6_E2QVH6_CANLF_9615 and tr_A0A2Y9LD99_A0A2Y9LD99_ENHLU_391180 are exactly identical! WARNING: Sequences sp_O43293_DAPK3_HUMAN_9606 and tr_A0A0A0MVV4_A0A0A0MVV4_PAPAN_9555 are exactly identical! WARNING: Sequences sp_O43293_DAPK3_HUMAN_9606 and tr_A0A0D9REQ5_A0A0D9REQ5_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q9H1R3_MYLK2_HUMAN_9606 and tr_A0A2R9C2Z8_A0A2R9C2Z8_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q9UIK4_DAPK2_HUMAN_9606 and tr_A0A2R9BC39_A0A2R9BC39_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5R7Y5_A0A1D5R7Y5_MACMU_9544 and tr_G7P8U1_G7P8U1_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5RJR8_A0A1D5RJR8_MACMU_9544 and tr_G7PSM8_G7PSM8_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5RJR8_A0A1D5RJR8_MACMU_9544 and tr_A0A2K5YSC4_A0A2K5YSC4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0Q9WY93_A0A0Q9WY93_DROVI_7244 and tr_D0Z7E3_D0Z7E3_DROVI_7244 are exactly identical! WARNING: Sequences tr_G7PGN7_G7PGN7_MACFA_9541 and tr_A0A2K6C4U2_A0A2K6C4U2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3LV46_A0A2I3LV46_PAPAN_9555 and tr_A0A2K5NYB9_A0A2K5NYB9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LV46_A0A2I3LV46_PAPAN_9555 and tr_A0A2K5YTB3_A0A2K5YTB3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091F0K4_A0A091F0K4_CORBR_85066 and tr_A0A093Q7U7_A0A093Q7U7_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091F0K4_A0A091F0K4_CORBR_85066 and tr_A0A091W2W7_A0A091W2W7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091F0K4_A0A091F0K4_CORBR_85066 and tr_A0A091W970_A0A091W970_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091F0K4_A0A091F0K4_CORBR_85066 and tr_A0A091HJU6_A0A091HJU6_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A087R5N9_A0A087R5N9_APTFO_9233 and tr_A0A093HUF9_A0A093HUF9_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A087R5N9_A0A087R5N9_APTFO_9233 and tr_A0A099ZRV1_A0A099ZRV1_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A087R5N9_A0A087R5N9_APTFO_9233 and tr_A0A0A0AVW0_A0A0A0AVW0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0A0ALW3_A0A0A0ALW3_CHAVO_50402 and tr_A0A093GAC9_A0A093GAC9_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A2Y9LTT8_A0A2Y9LTT8_DELLE_9749 and tr_A0A383Z2C1_A0A383Z2C1_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 27 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/Q15746/4_raxmlng_ancestral/Q15746.raxml.reduced.phy Alignment comprises 1 partitions and 1914 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1914 Gaps: 66.28 % Invariant sites: 0.05 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15746/4_raxmlng_ancestral/Q15746.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/Q15746/3_mltree/Q15746.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 479 / 38320 [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: -398493.090902 [00:00:01 -398493.090902] Initial branch length optimization [00:00:13 -374961.579830] Model parameter optimization (eps = 0.100000) [00:04:04] Tree #1, final logLikelihood: -373748.826959 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.069186,0.226673) (0.090007,0.286357) (0.318616,0.666930) (0.522192,1.428688) 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/Q15746/4_raxmlng_ancestral/Q15746.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15746/4_raxmlng_ancestral/Q15746.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15746/4_raxmlng_ancestral/Q15746.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q15746/4_raxmlng_ancestral/Q15746.raxml.log Analysis started: 03-Jun-2021 02:34:27 / finished: 03-Jun-2021 02:38:54 Elapsed time: 266.926 seconds Consumed energy: 13.184 Wh