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 13:36:23 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P35968/2_msa/P35968_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P35968/3_mltree/P35968.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P35968/4_raxmlng_ancestral/P35968 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802983 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/P35968/2_msa/P35968_nogap_msa.fasta [00:00:00] Loaded alignment with 997 taxa and 1356 sites WARNING: Sequences tr_F1P3S0_F1P3S0_CHICK_9031 and sp_P18460_FGFR3_CHICK_9031 are exactly identical! WARNING: Sequences tr_M3YE16_M3YE16_MUSPF_9669 and tr_A0A2Y9J985_A0A2Y9J985_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3QZ51_G3QZ51_GORGO_9595 and tr_H2Q2P3_H2Q2P3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QZ51_G3QZ51_GORGO_9595 and tr_A0A2R9B2V2_A0A2R9B2V2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RBC6_G3RBC6_GORGO_9595 and tr_A0A2I3RMA9_A0A2I3RMA9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RBC6_G3RBC6_GORGO_9595 and sp_P11362_FGFR1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RBC6_G3RBC6_GORGO_9595 and tr_A0A096MT31_A0A096MT31_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RBC6_G3RBC6_GORGO_9595 and tr_A0A2K5NV80_A0A2K5NV80_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2QPH6_H2QPH6_PANTR_9598 and tr_A0A2R9CED2_A0A2R9CED2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QYN7_A0A1D5QYN7_MACMU_9544 and tr_A0A2I3LIL7_A0A2I3LIL7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QYN7_A0A1D5QYN7_MACMU_9544 and tr_A0A0D9QXC2_A0A0D9QXC2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QYN7_A0A1D5QYN7_MACMU_9544 and tr_A0A2K5MTR7_A0A2K5MTR7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QYN7_A0A1D5QYN7_MACMU_9544 and tr_A0A2K5XUY7_A0A2K5XUY7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7MTB0_G7MTB0_MACMU_9544 and tr_A0A096N3T8_A0A096N3T8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7MTB0_G7MTB0_MACMU_9544 and tr_A0A2K6CFG2_A0A2K6CFG2_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZK19_H0ZK19_TAEGU_59729 and tr_A0A218V8P1_A0A218V8P1_9PASE_299123 are exactly identical! WARNING: Sequences tr_G7PE88_G7PE88_MACFA_9541 and tr_A0A2K6DJ09_A0A2K6DJ09_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A151NBT6_A0A151NBT6_ALLMI_8496 and tr_A0A3Q0GLX8_A0A3Q0GLX8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091VEL8_A0A091VEL8_NIPNI_128390 and tr_A0A091FPL7_A0A091FPL7_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A2D0Q0E5_A0A2D0Q0E5_ICTPU_7998 and tr_A0A2D0Q235_A0A2D0Q235_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0Q0E5_A0A2D0Q0E5_ICTPU_7998 and tr_W5UKQ9_W5UKQ9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QMB0_A0A2D0QMB0_ICTPU_7998 and tr_A0A2D0QQ00_A0A2D0QQ00_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QNJ8_A0A2D0QNJ8_ICTPU_7998 and tr_A0A2D0QRF5_A0A2D0QRF5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QNK2_A0A2D0QNK2_ICTPU_7998 and tr_A0A2D0QNT3_A0A2D0QNT3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QNK2_A0A2D0QNK2_ICTPU_7998 and tr_A0A2D0QP27_A0A2D0QP27_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QNK2_A0A2D0QNK2_ICTPU_7998 and tr_A0A2D0QP33_A0A2D0QP33_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QNK2_A0A2D0QNK2_ICTPU_7998 and tr_A0A2D0QQR3_A0A2D0QQR3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QXX4_A0A2D0QXX4_ICTPU_7998 and tr_A0A2D0QZH2_A0A2D0QZH2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RFC5_A0A2D0RFC5_ICTPU_7998 and tr_W5UHK1_W5UHK1_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 29 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/P35968/4_raxmlng_ancestral/P35968.raxml.reduced.phy Alignment comprises 1 partitions and 1356 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1356 Gaps: 34.57 % Invariant sites: 0.29 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P35968/4_raxmlng_ancestral/P35968.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/P35968/3_mltree/P35968.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 339 / 27120 [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: -505239.866557 [00:00:00 -505239.866557] Initial branch length optimization [00:00:04 -396663.997408] Model parameter optimization (eps = 0.100000) [00:01:48] Tree #1, final logLikelihood: -396251.111643 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.144481,0.171476) (0.151215,0.373130) (0.362115,0.894265) (0.342189,1.738734) 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/P35968/4_raxmlng_ancestral/P35968.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P35968/4_raxmlng_ancestral/P35968.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P35968/4_raxmlng_ancestral/P35968.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P35968/4_raxmlng_ancestral/P35968.raxml.log Analysis started: 04-Jun-2021 13:36:23 / finished: 04-Jun-2021 13:38:24 Elapsed time: 120.755 seconds