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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 04-Jun-2021 14:23:48 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q58F21/2_msa/Q58F21_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q58F21/3_mltree/Q58F21.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q58F21/4_raxmlng_ancestral/Q58F21 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805828 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q58F21/2_msa/Q58F21_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 947 sites WARNING: Sequences tr_A0A2I2Y8Z2_A0A2I2Y8Z2_GORGO_9595 and tr_A0A2I3TJC4_A0A2I3TJC4_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Y8Z2_A0A2I2Y8Z2_GORGO_9595 and sp_P25440_BRD2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_E2QW92_E2QW92_CANLF_9615 and tr_A0A2U3ZNW4_A0A2U3ZNW4_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2QW92_E2QW92_CANLF_9615 and tr_A0A2Y9J0A2_A0A2Y9J0A2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3TJ11_A0A2I3TJ11_PANTR_9598 and sp_O60885_BRD4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TJ11_A0A2I3TJ11_PANTR_9598 and tr_F7FHI3_F7FHI3_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3TJ11_A0A2I3TJ11_PANTR_9598 and tr_A0A2I3MW75_A0A2I3MW75_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2QY49_H2QY49_PANTR_9598 and sp_Q15059_BRD3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F7G2U9_F7G2U9_MACMU_9544 and tr_A0A0D9RSS2_A0A0D9RSS2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7G2U9_F7G2U9_MACMU_9544 and tr_A0A2K6C400_A0A2K6C400_MACNE_9545 are exactly identical! WARNING: Sequences tr_F4P1T9_F4P1T9_BATDJ_684364 and tr_A0A177WR49_A0A177WR49_BATDE_403673 are exactly identical! WARNING: Sequences tr_I1QAY8_I1QAY8_ORYGL_4538 and tr_A0A0D3GRF4_A0A0D3GRF4_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0Q8S5_A0A0E0Q8S5_ORYRU_4529 and tr_A0A0E0AKC9_A0A0E0AKC9_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A5D9K6_A5D9K6_PIG_9823 and tr_G1L580_G1L580_AILME_9646 are exactly identical! WARNING: Sequences tr_A5D9K6_A5D9K6_PIG_9823 and tr_A0A1U7TY33_A0A1U7TY33_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A5D9K6_A5D9K6_PIG_9823 and tr_A0A2U3WG99_A0A2U3WG99_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A067FKN7_A0A067FKN7_CITSI_2711 and tr_V4RNH7_V4RNH7_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A2I3MN57_A0A2I3MN57_PAPAN_9555 and tr_A0A2K5MC37_A0A2K5MC37_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MN57_A0A2I3MN57_PAPAN_9555 and tr_A0A2K6A8M8_A0A2K6A8M8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A094E0N1_A0A094E0N1_9PEZI_1420912 and tr_A0A1B8GLT9_A0A1B8GLT9_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A2I0M3Q8_A0A2I0M3Q8_COLLI_8932 and tr_A0A1V4J652_A0A1V4J652_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3ZWA3_A0A1S3ZWA3_TOBAC_4097 and tr_A0A1U7YX65_A0A1U7YX65_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A226MCM5_A0A226MCM5_CALSU_9009 and tr_A0A226P4V3_A0A226P4V3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PRC2_A0A2D0PRC2_ICTPU_7998 and tr_W5U5R8_W5U5R8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PU48_A0A2D0PU48_ICTPU_7998 and tr_A0A2D0PU53_A0A2D0PU53_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PU48_A0A2D0PU48_ICTPU_7998 and tr_A0A2D0PVK0_A0A2D0PVK0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PU48_A0A2D0PU48_ICTPU_7998 and tr_A0A2D0PVL7_A0A2D0PVL7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PU48_A0A2D0PU48_ICTPU_7998 and tr_A0A2D0PVM2_A0A2D0PVM2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PU48_A0A2D0PU48_ICTPU_7998 and tr_A0A2D0PXB0_A0A2D0PXB0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PU48_A0A2D0PU48_ICTPU_7998 and tr_A0A2D0PY73_A0A2D0PY73_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K6BKD1_A0A2K6BKD1_MACNE_9545 and tr_A0A2K5ZWD0_A0A2K5ZWD0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2Y9NWG8_A0A2Y9NWG8_DELLE_9749 and tr_A0A384AHZ8_A0A384AHZ8_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 32 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q58F21/4_raxmlng_ancestral/Q58F21.raxml.reduced.phy Alignment comprises 1 partitions and 947 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 947 Gaps: 44.69 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q58F21/4_raxmlng_ancestral/Q58F21.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q58F21/3_mltree/Q58F21.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 237 / 18960 [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: -335799.283546 [00:00:00 -335799.283546] Initial branch length optimization [00:00:02 -325734.819183] Model parameter optimization (eps = 0.100000) [00:00:59] Tree #1, final logLikelihood: -324372.243158 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.080260,0.412768) (0.040646,0.457756) (0.290877,0.615462) (0.588217,1.307752) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q58F21/4_raxmlng_ancestral/Q58F21.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q58F21/4_raxmlng_ancestral/Q58F21.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q58F21/4_raxmlng_ancestral/Q58F21.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q58F21/4_raxmlng_ancestral/Q58F21.raxml.log Analysis started: 04-Jun-2021 14:23:48 / finished: 04-Jun-2021 14:24:56 Elapsed time: 67.519 seconds