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 02:47:24 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43526/2_msa/O43526_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43526/3_mltree/O43526.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43526/4_raxmlng_ancestral/O43526 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677644 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/O43526/2_msa/O43526_nogap_msa.fasta [00:00:00] Loaded alignment with 975 taxa and 872 sites WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A091XL48_A0A091XL48_OPIHO_30419 are exactly identical! WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A099ZVZ5_A0A099ZVZ5_CHAVO_50402 are exactly identical! WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A2I0MKC3_A0A2I0MKC3_COLLI_8932 are exactly identical! WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A1V4K8E8_A0A1V4K8E8_PATFA_372326 are exactly identical! WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A226MDZ7_A0A226MDZ7_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A226PJZ6_A0A226PJZ6_COLVI_9014 are exactly identical! WARNING: Sequences sp_P16388_KCNA1_MOUSE_10090 and tr_G3GUL0_G3GUL0_CRIGR_10029 are exactly identical! WARNING: Sequences tr_M3Z617_M3Z617_MUSPF_9669 and tr_F1PKN8_F1PKN8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z617_M3Z617_MUSPF_9669 and tr_M3W515_M3W515_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z617_M3Z617_MUSPF_9669 and tr_A0A2U3WVM7_A0A2U3WVM7_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z617_M3Z617_MUSPF_9669 and tr_A0A2U3Z2P4_A0A2U3Z2P4_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Z617_M3Z617_MUSPF_9669 and tr_A0A2Y9KVN5_A0A2Y9KVN5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1SB08_G1SB08_NOMLE_61853 and tr_G3S108_G3S108_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1SB08_G1SB08_NOMLE_61853 and tr_H2NG69_H2NG69_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1SB08_G1SB08_NOMLE_61853 and tr_H2Q593_H2Q593_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1SB08_G1SB08_NOMLE_61853 and sp_Q09470_KCNA1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1SB08_G1SB08_NOMLE_61853 and tr_F7DS72_F7DS72_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1SB08_G1SB08_NOMLE_61853 and tr_A0A096N578_A0A096N578_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1SB08_G1SB08_NOMLE_61853 and tr_A0A0D9SCZ1_A0A0D9SCZ1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1SB08_G1SB08_NOMLE_61853 and tr_A0A2K5KMH7_A0A2K5KMH7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1SB08_G1SB08_NOMLE_61853 and tr_A0A2K6AM91_A0A2K6AM91_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1SB08_G1SB08_NOMLE_61853 and tr_A0A2K5XFR1_A0A2K5XFR1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1SB08_G1SB08_NOMLE_61853 and tr_A0A2R8ZFZ7_A0A2R8ZFZ7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R701_G3R701_GORGO_9595 and tr_A0A2I3S1D1_A0A2I3S1D1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R701_G3R701_GORGO_9595 and tr_A0A2R9C3J4_A0A2R9C3J4_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7EBT4_F7EBT4_MONDO_13616 and tr_G3W9V6_G3W9V6_SARHA_9305 are exactly identical! WARNING: Sequences tr_H0V383_H0V383_CAVPO_10141 and tr_G5ARZ7_G5ARZ7_HETGA_10181 are exactly identical! WARNING: Sequences tr_F7DI95_F7DI95_MACMU_9544 and tr_A0A2K5NHH6_A0A2K5NHH6_CERAT_9531 are exactly identical! WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_U3KKD6_U3KKD6_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_A0A093HQ36_A0A093HQ36_STRCA_441894 are exactly identical! WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_A0A093GUI1_A0A093GUI1_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_A0A091JAH5_A0A091JAH5_CALAN_9244 are exactly identical! WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_A0A218UFS4_A0A218UFS4_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A091JQX9_A0A091JQX9_EGRGA_188379 and tr_A0A091VQM5_A0A091VQM5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091VLI6_A0A091VLI6_NIPNI_128390 and tr_A0A091G6X5_A0A091G6X5_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091WIM2_A0A091WIM2_OPIHO_30419 and tr_A0A099ZF49_A0A099ZF49_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A0V0VKP7_A0A0V0VKP7_9BILA_181606 and tr_A0A0V1PHR2_A0A0V1PHR2_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0ZMT8_A0A0V0ZMT8_9BILA_990121 and tr_A0A0V1NPM6_A0A0V1NPM6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0ZMT8_A0A0V0ZMT8_9BILA_990121 and tr_A0A0V0TNR6_A0A0V0TNR6_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A2D0RW07_A0A2D0RW07_ICTPU_7998 and tr_A0A2D0RWX1_A0A2D0RWX1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5L5Z3_A0A2K5L5Z3_CERAT_9531 and tr_A0A2K6DCZ5_A0A2K6DCZ5_MACNE_9545 are exactly identical! WARNING: Duplicate sequences found: 41 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/O43526/4_raxmlng_ancestral/O43526.raxml.reduced.phy Alignment comprises 1 partitions and 872 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 872 Gaps: 44.59 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43526/4_raxmlng_ancestral/O43526.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/O43526/3_mltree/O43526.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 218 / 17440 [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: -324299.742776 [00:00:00 -324299.742776] Initial branch length optimization [00:00:02 -216310.651994] Model parameter optimization (eps = 0.100000) [00:01:25] Tree #1, final logLikelihood: -215468.110276 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.173666,0.284259) (0.159271,0.367178) (0.275346,0.725002) (0.391716,1.767930) 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/O43526/4_raxmlng_ancestral/O43526.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43526/4_raxmlng_ancestral/O43526.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43526/4_raxmlng_ancestral/O43526.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O43526/4_raxmlng_ancestral/O43526.raxml.log Analysis started: 03-Jun-2021 02:47:24 / finished: 03-Jun-2021 02:48:58 Elapsed time: 93.474 seconds Consumed energy: 7.852 Wh