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 23-Jun-2021 00:33:06 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P00439/2_msa/P00439_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P00439/3_mltree/P00439.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P00439/4_raxmlng_ancestral/P00439 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624397586 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/030621_run/phylogeny-snakemake/results/P00439/2_msa/P00439_nogap_msa.fasta [00:00:00] Loaded alignment with 948 taxa and 452 sites WARNING: Sequences tr_B4QKX6_B4QKX6_DROSI_7240 and tr_B4HIV9_B4HIV9_DROSE_7238 are exactly identical! WARNING: Sequences tr_Q29DP1_Q29DP1_DROPS_46245 and tr_B4HDG7_B4HDG7_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29DR7_Q29DR7_DROPS_46245 and tr_B4H7A4_B4H7A4_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2I3SMD3_A0A2I3SMD3_PANTR_9598 and sp_P17752_TPH1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TG35_A0A2I3TG35_PANTR_9598 and tr_A0A2R9ACE6_A0A2R9ACE6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q6R0_H2Q6R0_PANTR_9598 and tr_A0A2R8ZCI5_A0A2R8ZCI5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NFE8_A0A158NFE8_ATTCE_12957 and tr_A0A195BDE8_A0A195BDE8_9HYME_520822 are exactly identical! WARNING: Sequences sp_P07101_TY3H_HUMAN_9606 and tr_A0A2R9BMK2_A0A2R9BMK2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0K0JGS3_A0A0K0JGS3_BRUMA_6279 and tr_A0A0R3QMZ7_A0A0R3QMZ7_9BILA_42155 are exactly identical! WARNING: Sequences tr_F7C904_F7C904_MACMU_9544 and sp_Q2HZ26_TPH2_MACMU_9544 are exactly identical! WARNING: Sequences tr_F7C904_F7C904_MACMU_9544 and tr_G7PI25_G7PI25_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7C904_F7C904_MACMU_9544 and tr_A0A096N129_A0A096N129_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7C904_F7C904_MACMU_9544 and tr_A0A2K6CT63_A0A2K6CT63_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7C904_F7C904_MACMU_9544 and tr_A0A2K5XAH0_A0A2K5XAH0_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7PJC2_G7PJC2_MACFA_9541 and tr_A0A0D9S1L9_A0A0D9S1L9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7PJC2_G7PJC2_MACFA_9541 and tr_A0A2K5NEI1_A0A2K5NEI1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PJC2_G7PJC2_MACFA_9541 and tr_A0A2K6BHX1_A0A2K6BHX1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PJC2_G7PJC2_MACFA_9541 and tr_A0A2K5ZL20_A0A2K5ZL20_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A015II88_A0A015II88_9GLOM_1432141 and tr_U9U2V0_U9U2V0_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A0A1NKF8_A0A0A1NKF8_9FUNG_58291 and tr_A0A367JH87_A0A367JH87_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A087QQ97_A0A087QQ97_APTFO_9233 and tr_A0A0A0ANT4_A0A0A0ANT4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1CS64_A0A0V1CS64_TRIBR_45882 and tr_A0A0V0X3H3_A0A0V0X3H3_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CS64_A0A0V1CS64_TRIBR_45882 and tr_A0A0V0VVD5_A0A0V0VVD5_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CS64_A0A0V1CS64_TRIBR_45882 and tr_A0A0V1P0A3_A0A0V1P0A3_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1KRG9_A0A0V1KRG9_9BILA_6335 and tr_A0A0V1NX69_A0A0V1NX69_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1I7U5E9_A0A1I7U5E9_9PELO_1561998 and tr_A0A1I7U5F0_A0A1I7U5F0_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1I7U5E9_A0A1I7U5E9_9PELO_1561998 and tr_A0A1I7U5F1_A0A1I7U5F1_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1D1W9A6_A0A1D1W9A6_RAMVA_947166 and tr_A0A1D1W9G8_A0A1D1W9G8_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A226N7S7_A0A226N7S7_CALSU_9009 and tr_A0A226P313_A0A226P313_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QQX5_A0A2D0QQX5_ICTPU_7998 and tr_A0A2D0QT84_A0A2D0QT84_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K6CVW6_A0A2K6CVW6_MACNE_9545 and tr_A0A2K5YX17_A0A2K5YX17_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 31 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P00439/4_raxmlng_ancestral/P00439.raxml.reduced.phy Alignment comprises 1 partitions and 452 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 452 Gaps: 12.77 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P00439/4_raxmlng_ancestral/P00439.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/030621_run/phylogeny-snakemake/results/P00439/3_mltree/P00439.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 113 / 9040 [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: -166149.500009 [00:00:00 -166149.500009] Initial branch length optimization [00:00:00 -165790.180754] Model parameter optimization (eps = 0.100000) [00:00:23] Tree #1, final logLikelihood: -165182.172095 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.222561,0.316767) (0.254112,0.443085) (0.256058,1.012417) (0.267268,2.086550) 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/030621_run/phylogeny-snakemake/results/P00439/4_raxmlng_ancestral/P00439.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P00439/4_raxmlng_ancestral/P00439.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P00439/4_raxmlng_ancestral/P00439.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P00439/4_raxmlng_ancestral/P00439.raxml.log Analysis started: 23-Jun-2021 00:33:06 / finished: 23-Jun-2021 00:33:33 Elapsed time: 27.426 seconds Consumed energy: 2.202 Wh