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 02:56:32 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07949/2_msa/P07949_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07949/3_mltree/P07949.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07949/4_raxmlng_ancestral/P07949 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622678192 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/P07949/2_msa/P07949_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1114 sites WARNING: Sequences tr_F1P3S0_F1P3S0_CHICK_9031 and sp_P18460_FGFR3_CHICK_9031 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 sp_P11362_FGFR1_HUMAN_9606 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_F7E313_F7E313_MACMU_9544 and tr_A0A2K6DVH4_A0A2K6DVH4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FAY2_F7FAY2_MACMU_9544 and tr_A0A2K5M967_A0A2K5M967_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3TKE5_G3TKE5_LOXAF_9785 and tr_L5KB29_L5KB29_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G7PE88_G7PE88_MACFA_9541 and tr_A0A2K6DJ09_A0A2K6DJ09_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096N6L3_A0A096N6L3_PAPAN_9555 and tr_A0A2K5XX73_A0A2K5XX73_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151NBT6_A0A151NBT6_ALLMI_8496 and tr_A0A3Q0GLX8_A0A3Q0GLX8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091JGY4_A0A091JGY4_EGRGA_188379 and tr_A0A091VXG5_A0A091VXG5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JI37_A0A091JI37_EGRGA_188379 and tr_A0A091W6X5_A0A091W6X5_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JI37_A0A091JI37_EGRGA_188379 and tr_A0A0A0AE48_A0A0A0AE48_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091VEL8_A0A091VEL8_NIPNI_128390 and tr_A0A091FPL7_A0A091FPL7_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091VZV5_A0A091VZV5_NIPNI_128390 and tr_A0A0A0ALR8_A0A0A0ALR8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1S3NJQ6_A0A1S3NJQ6_SALSA_8030 and tr_A0A060VNI8_A0A060VNI8_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A2D0Q2J2_A0A2D0Q2J2_ICTPU_7998 and tr_A0A2D0Q3G5_A0A2D0Q3G5_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_A0A2D0QP33_A0A2D0QP33_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QNT3_A0A2D0QNT3_ICTPU_7998 and tr_A0A2D0QP27_A0A2D0QP27_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QNT3_A0A2D0QNT3_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_A0A2D0T1D5_A0A2D0T1D5_ICTPU_7998 and tr_W5UG95_W5UG95_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5L771_A0A2K5L771_CERAT_9531 and tr_A0A2K5ZP61_A0A2K5ZP61_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/020621_run/phylogeny-snakemake/results/P07949/4_raxmlng_ancestral/P07949.raxml.reduced.phy Alignment comprises 1 partitions and 1114 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1114 Gaps: 42.05 % Invariant sites: 0.63 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07949/4_raxmlng_ancestral/P07949.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/P07949/3_mltree/P07949.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 279 / 22320 [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: -304262.284063 [00:00:00 -304262.284063] Initial branch length optimization [00:00:01 -303233.293933] Model parameter optimization (eps = 0.100000) [00:01:15] Tree #1, final logLikelihood: -302556.564542 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.101035,0.173347) (0.090703,0.210556) (0.388862,0.711067) (0.419400,1.637770) 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/P07949/4_raxmlng_ancestral/P07949.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07949/4_raxmlng_ancestral/P07949.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07949/4_raxmlng_ancestral/P07949.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07949/4_raxmlng_ancestral/P07949.raxml.log Analysis started: 03-Jun-2021 02:56:32 / finished: 03-Jun-2021 02:57:58 Elapsed time: 85.439 seconds Consumed energy: 7.172 Wh