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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 23-Jun-2021 00:29:51 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P02545/2_msa/P02545_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P02545/3_mltree/P02545.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P02545/4_raxmlng_ancestral/P02545 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624397391 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/P02545/2_msa/P02545_nogap_msa.fasta [00:00:00] Loaded alignment with 809 taxa and 664 sites WARNING: Sequences tr_M3YT34_M3YT34_MUSPF_9669 and tr_A0A2Y9KVQ1_A0A2Y9KVQ1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3QEU9_G3QEU9_GORGO_9595 and sp_P02545_LMNA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QJS0_G3QJS0_GORGO_9595 and sp_P17661_DESM_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RNG2_G3RNG2_GORGO_9595 and sp_Q5R408_NFL_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RNG2_G3RNG2_GORGO_9595 and tr_A0A2I3SJH8_A0A2I3SJH8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RNG2_G3RNG2_GORGO_9595 and sp_P07196_NFL_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RNG2_G3RNG2_GORGO_9595 and tr_A0A2R9BTF6_A0A2R9BTF6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RWL2_G3RWL2_GORGO_9595 and tr_H2PGE3_H2PGE3_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3SHE6_G3SHE6_GORGO_9595 and tr_H2Q5V1_H2Q5V1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SHE6_G3SHE6_GORGO_9595 and sp_P41219_PERI_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SHE6_G3SHE6_GORGO_9595 and tr_A0A2R9AZE7_A0A2R9AZE7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q091_H2Q091_PANTR_9598 and tr_A0A2R9BK07_A0A2R9BK07_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QRE7_H2QRE7_PANTR_9598 and tr_A0A2R9BUC3_A0A2R9BUC3_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5QG29_W5QG29_SHEEP_9940 and sp_P02540_DESM_PIG_9823 are exactly identical! WARNING: Sequences tr_W5QG29_W5QG29_SHEEP_9940 and sp_O62654_DESM_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5QG29_W5QG29_SHEEP_9940 and tr_A0A337SLT6_A0A337SLT6_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A1D5QQZ2_A0A1D5QQZ2_MACMU_9544 and tr_G7NV78_G7NV78_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QQZ2_A0A1D5QQZ2_MACMU_9544 and tr_A0A096MQV4_A0A096MQV4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QQZ2_A0A1D5QQZ2_MACMU_9544 and tr_A0A0D9S4Z6_A0A0D9S4Z6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QQZ2_A0A1D5QQZ2_MACMU_9544 and tr_A0A2K6ED46_A0A2K6ED46_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QQZ2_A0A1D5QQZ2_MACMU_9544 and tr_A0A2K5YDB4_A0A2K5YDB4_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6R7X5_F6R7X5_MACMU_9544 and tr_A0A0A0MV39_A0A0A0MV39_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6R7X5_F6R7X5_MACMU_9544 and tr_A0A2K6DZV2_A0A2K6DZV2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7ED68_F7ED68_MACMU_9544 and tr_A0A2K6DB76_A0A2K6DB76_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7ED68_F7ED68_MACMU_9544 and tr_A0A2K5XH32_A0A2K5XH32_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7ERR2_F7ERR2_MACMU_9544 and tr_B0CM49_B0CM49_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7ERR2_F7ERR2_MACMU_9544 and tr_A0A0D9R6T4_A0A0D9R6T4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7ERR2_F7ERR2_MACMU_9544 and tr_A0A2K5LDT7_A0A2K5LDT7_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7ERR2_F7ERR2_MACMU_9544 and tr_A0A2K6D3R9_A0A2K6D3R9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7ERR2_F7ERR2_MACMU_9544 and tr_A0A2K5YQE7_A0A2K5YQE7_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7G5S6_F7G5S6_MACMU_9544 and tr_A0A096NJD8_A0A096NJD8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7G5S6_F7G5S6_MACMU_9544 and tr_A0A2K6DE45_A0A2K6DE45_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GW66_F7GW66_MACMU_9544 and tr_A0A2K5N8A5_A0A2K5N8A5_CERAT_9531 are exactly identical! WARNING: Sequences tr_H0ZJ23_H0ZJ23_TAEGU_59729 and tr_U3K279_U3K279_FICAL_59894 are exactly identical! WARNING: Sequences tr_A0A096MS49_A0A096MS49_PAPAN_9555 and tr_A0A0D9RPS0_A0A0D9RPS0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MS49_A0A096MS49_PAPAN_9555 and tr_A0A2K5MBU6_A0A2K5MBU6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MS49_A0A096MS49_PAPAN_9555 and tr_A0A2K6CEN3_A0A2K6CEN3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NAQ5_A0A096NAQ5_PAPAN_9555 and tr_A0A0D9R1E9_A0A0D9R1E9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NAQ5_A0A096NAQ5_PAPAN_9555 and tr_A0A2K6C7C4_A0A2K6C7C4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NAQ5_A0A096NAQ5_PAPAN_9555 and tr_A0A2K5Y3J4_A0A2K5Y3J4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0V1CK15_A0A0V1CK15_TRIBR_45882 and tr_A0A0V0VIX6_A0A0V0VIX6_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CK15_A0A0V1CK15_TRIBR_45882 and tr_A0A0V1KPB8_A0A0V1KPB8_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CK15_A0A0V1CK15_TRIBR_45882 and tr_A0A0V0ZJC8_A0A0V0ZJC8_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1DCK0_A0A0V1DCK0_TRIBR_45882 and tr_A0A0V1P2S4_A0A0V1P2S4_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0W5T3_A0A0V0W5T3_9BILA_92179 and tr_A0A0V1NQ44_A0A0V1NQ44_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0W5T3_A0A0V0W5T3_9BILA_92179 and tr_A0A0V0TDR8_A0A0V0TDR8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3GYA9_A0A1S3GYA9_LINUN_7574 and tr_A0A1S3GYJ9_A0A1S3GYJ9_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A226NN62_A0A226NN62_CALSU_9009 and tr_A0A226PAN0_A0A226PAN0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0SRK4_A0A2D0SRK4_ICTPU_7998 and tr_A0A2D0SRK8_A0A2D0SRK8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SRK4_A0A2D0SRK4_ICTPU_7998 and tr_A0A2D0SSP3_A0A2D0SSP3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4BAE0_A0A2U4BAE0_TURTR_9739 and tr_A0A2Y9N997_A0A2Y9N997_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3W436_A0A2U3W436_ODORO_9708 and tr_A0A2U3Y7N6_A0A2U3Y7N6_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 52 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/P02545/4_raxmlng_ancestral/P02545.raxml.reduced.phy Alignment comprises 1 partitions and 664 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 664 Gaps: 30.84 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P02545/4_raxmlng_ancestral/P02545.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/P02545/3_mltree/P02545.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 166 / 13280 [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: -222105.765133 [00:00:00 -222105.765133] Initial branch length optimization [00:00:02 -199100.091053] Model parameter optimization (eps = 0.100000) [00:00:56] Tree #1, final logLikelihood: -198121.932665 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.140051,0.570094) (0.090365,1.066924) (0.476051,0.813286) (0.293533,1.487325) 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/P02545/4_raxmlng_ancestral/P02545.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P02545/4_raxmlng_ancestral/P02545.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P02545/4_raxmlng_ancestral/P02545.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P02545/4_raxmlng_ancestral/P02545.raxml.log Analysis started: 23-Jun-2021 00:29:51 / finished: 23-Jun-2021 00:30:53 Elapsed time: 61.139 seconds Consumed energy: 4.217 Wh