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 17:23:20 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q969G3/2_msa/Q969G3_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q969G3/3_mltree/Q969G3.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q969G3/4_raxmlng_ancestral/Q969G3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099800 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/Q969G3/2_msa/Q969G3_nogap_msa.fasta [00:00:00] Loaded alignment with 699 taxa and 411 sites WARNING: Sequences tr_G1QNI4_G1QNI4_NOMLE_61853 and tr_A0A2J8WAE4_A0A2J8WAE4_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QNI4_G1QNI4_NOMLE_61853 and tr_A0A2I3RU20_A0A2I3RU20_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QNI4_G1QNI4_NOMLE_61853 and sp_Q969G3_SMCE1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QNI4_G1QNI4_NOMLE_61853 and tr_A0A2K5M1A0_A0A2K5M1A0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QNI4_G1QNI4_NOMLE_61853 and tr_A0A2K6ASS5_A0A2K6ASS5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QNI4_G1QNI4_NOMLE_61853 and tr_A0A2K5Z3Q1_A0A2K5Z3Q1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3R158_G3R158_GORGO_9595 and sp_O15405_TOX3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7CYZ5_K7CYZ5_PANTR_9598 and sp_Q9P0W2_HM20B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7CYZ5_K7CYZ5_PANTR_9598 and tr_A0A0A0MU69_A0A0A0MU69_PAPAN_9555 are exactly identical! WARNING: Sequences tr_K7CYZ5_K7CYZ5_PANTR_9598 and tr_A0A0D9RFG5_A0A0D9RFG5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_K7CYZ5_K7CYZ5_PANTR_9598 and tr_A0A2K6CY00_A0A2K6CY00_MACNE_9545 are exactly identical! WARNING: Sequences tr_K7CYZ5_K7CYZ5_PANTR_9598 and tr_A0A2R9CDQ1_A0A2R9CDQ1_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7BMM9_F7BMM9_MONDO_13616 and tr_G3WVU6_G3WVU6_SARHA_9305 are exactly identical! WARNING: Sequences tr_A0A158N903_A0A158N903_ATTCE_12957 and tr_A0A151I192_A0A151I192_9HYME_520822 are exactly identical! WARNING: Sequences tr_F6S6N6_F6S6N6_MACMU_9544 and tr_G7Q143_G7Q143_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6S6N6_F6S6N6_MACMU_9544 and tr_A0A2I3NBJ6_A0A2I3NBJ6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6S6N6_F6S6N6_MACMU_9544 and tr_A0A2K5KM48_A0A2K5KM48_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6S6N6_F6S6N6_MACMU_9544 and tr_A0A2K6BSC2_A0A2K6BSC2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6S6N6_F6S6N6_MACMU_9544 and tr_A0A2K5XGA6_A0A2K5XGA6_MANLE_9568 are exactly identical! WARNING: Sequences tr_F4P6F8_F4P6F8_BATDJ_684364 and tr_A0A177WQX9_A0A177WQX9_BATDE_403673 are exactly identical! WARNING: Sequences tr_G3TCN0_G3TCN0_LOXAF_9785 and tr_A0A2Y9EA95_A0A2Y9EA95_TRIMA_127582 are exactly identical! WARNING: Sequences tr_U5HJI0_U5HJI0_USTV1_683840 and tr_A0A2X0P8D7_A0A2X0P8D7_9BASI_796604 are exactly identical! WARNING: Sequences tr_V2Y0J5_V2Y0J5_MONRO_1381753 and tr_A0A0W0FKD3_A0A0W0FKD3_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A0A1MTG4_A0A0A1MTG4_9FUNG_58291 and tr_A0A2G4SGK9_A0A2G4SGK9_9FUNG_1340429 are exactly identical! WARNING: Sequences tr_A0A0A1MTG4_A0A0A1MTG4_9FUNG_58291 and tr_A0A367J788_A0A367J788_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1NSY6_A0A0A1NSY6_9FUNG_58291 and tr_A0A367J217_A0A367J217_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A151NGM6_A0A151NGM6_ALLMI_8496 and tr_A0A3Q0H100_A0A3Q0H100_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151PC75_A0A151PC75_ALLMI_8496 and tr_A0A1U8DCN7_A0A1U8DCN7_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091WXH2_A0A091WXH2_NIPNI_128390 and tr_A0A087QXR9_A0A087QXR9_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A0V1DHK9_A0A0V1DHK9_TRIBR_45882 and tr_A0A0V0VYC7_A0A0V0VYC7_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A1V8UUA1_A0A1V8UUA1_9PEZI_1974281 and tr_A0A1V8SQ25_A0A1V8SQ25_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A2D0QEW6_A0A2D0QEW6_ICTPU_7998 and tr_A0A2D0QFX8_A0A2D0QFX8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QEW6_A0A2D0QEW6_ICTPU_7998 and tr_A0A2D0QFY0_A0A2D0QFY0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QEW6_A0A2D0QEW6_ICTPU_7998 and tr_A0A2D0QHB7_A0A2D0QHB7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QEW6_A0A2D0QEW6_ICTPU_7998 and tr_A0A2D0QHC2_A0A2D0QHC2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QEW6_A0A2D0QEW6_ICTPU_7998 and tr_A0A2D0QI75_A0A2D0QI75_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T3D7_A0A2D0T3D7_ICTPU_7998 and tr_A0A2D0T3F1_A0A2D0T3F1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T3D7_A0A2D0T3D7_ICTPU_7998 and tr_A0A2D0T3F3_A0A2D0T3F3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T3G5_A0A2D0T3G5_ICTPU_7998 and tr_A0A2D0T3N9_A0A2D0T3N9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3V7W3_A0A2U3V7W3_TURTR_9739 and tr_A0A2Y9LX12_A0A2Y9LX12_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 40 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/Q969G3/4_raxmlng_ancestral/Q969G3.raxml.reduced.phy Alignment comprises 1 partitions and 411 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 411 Gaps: 40.06 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q969G3/4_raxmlng_ancestral/Q969G3.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/Q969G3/3_mltree/Q969G3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 103 / 8240 [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: -104329.094639 [00:00:00 -104329.094639] Initial branch length optimization [00:00:00 -98420.638174] Model parameter optimization (eps = 0.100000) [00:01:07] Tree #1, final logLikelihood: -98159.218828 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.058478,0.371937) (0.062887,0.762904) (0.293852,0.518528) (0.584783,1.330242) 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/Q969G3/4_raxmlng_ancestral/Q969G3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q969G3/4_raxmlng_ancestral/Q969G3.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q969G3/4_raxmlng_ancestral/Q969G3.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q969G3/4_raxmlng_ancestral/Q969G3.raxml.log Analysis started: 12-Jul-2021 17:23:20 / finished: 12-Jul-2021 17:24:30 Elapsed time: 69.831 seconds Consumed energy: 6.082 Wh