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 17:19:23 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96MG7/2_msa/Q96MG7_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96MG7/3_mltree/Q96MG7.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96MG7/4_raxmlng_ancestral/Q96MG7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099563 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/Q96MG7/2_msa/Q96MG7_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 304 sites WARNING: Sequences tr_A0A2I3GXT4_A0A2I3GXT4_NOMLE_61853 and tr_A0A2I2YSZ8_A0A2I2YSZ8_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S2K2_G1S2K2_NOMLE_61853 and tr_G3QIN6_G3QIN6_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S2K2_G1S2K2_NOMLE_61853 and tr_A0A2R9BXN3_A0A2R9BXN3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3S4X5_G3S4X5_GORGO_9595 and sp_Q9Y5V3_MAGD1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S4X5_G3S4X5_GORGO_9595 and tr_F7HFL1_F7HFL1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3S4X5_G3S4X5_GORGO_9595 and tr_A0A2I3N239_A0A2I3N239_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3S4X5_G3S4X5_GORGO_9595 and tr_A0A0D9RJT1_A0A0D9RJT1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3S4X5_G3S4X5_GORGO_9595 and tr_A0A2K6BW41_A0A2K6BW41_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3S4X5_G3S4X5_GORGO_9595 and tr_A0A2K5YSE1_A0A2K5YSE1_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2NML2_H2NML2_PONAB_9601 and sp_Q99608_NECD_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3RS23_A0A2I3RS23_PANTR_9598 and tr_A0A2J8ILL3_A0A2J8ILL3_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3RS23_A0A2I3RS23_PANTR_9598 and tr_A0A2R9A741_A0A2R9A741_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SLD8_A0A2I3SLD8_PANTR_9598 and tr_A0A2R9BHS6_A0A2R9BHS6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SX08_A0A2I3SX08_PANTR_9598 and tr_A0A2J8JLA7_A0A2J8JLA7_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2J8IKX4_A0A2J8IKX4_PANTR_9598 and sp_Q96JG8_MAGD4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8IKX4_A0A2J8IKX4_PANTR_9598 and tr_A0A2R9CB18_A0A2R9CB18_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8L3B6_A0A2J8L3B6_PANTR_9598 and tr_A0A2R8ZNL5_A0A2R8ZNL5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8L3C9_A0A2J8L3C9_PANTR_9598 and tr_A0A2R8Z7Y2_A0A2R8Z7Y2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QNW0_H2QNW0_PANTR_9598 and tr_A0A2R8ZRZ5_A0A2R8ZRZ5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QYF3_H2QYF3_PANTR_9598 and tr_A0A2R8ZFE5_A0A2R8ZFE5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QYF7_H2QYF7_PANTR_9598 and tr_A0A2R8Z756_A0A2R8Z756_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QYG1_H2QYG1_PANTR_9598 and tr_A0A2R9BBM4_A0A2R9BBM4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QZ87_H2QZ87_PANTR_9598 and tr_A0A2R8Z8F4_A0A2R8Z8F4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R4N6_H2R4N6_PANTR_9598 and sp_Q9HCI5_MAGE1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7B4B1_K7B4B1_PANTR_9598 and tr_A0A2R9BW42_A0A2R9BW42_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5RA99_A0A1D5RA99_MACMU_9544 and tr_G7Q2S1_G7Q2S1_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5RA99_A0A1D5RA99_MACMU_9544 and tr_A0A0D9RJS1_A0A0D9RJS1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5RA99_A0A1D5RA99_MACMU_9544 and tr_A0A2K6C221_A0A2K6C221_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6TEU0_F6TEU0_MACMU_9544 and tr_G7Q2E5_G7Q2E5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6U8Q6_F6U8Q6_MACMU_9544 and tr_G7Q2F1_G7Q2F1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6VBW8_F6VBW8_MACMU_9544 and tr_A0A096N747_A0A096N747_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6VBW8_F6VBW8_MACMU_9544 and tr_A0A2K5N609_A0A2K5N609_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7D5S3_F7D5S3_MACMU_9544 and tr_A0A096NB08_A0A096NB08_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7D5S3_F7D5S3_MACMU_9544 and tr_A0A2K6CXP0_A0A2K6CXP0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7E9N0_F7E9N0_MACMU_9544 and tr_G7Q2U1_G7Q2U1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7E9N0_F7E9N0_MACMU_9544 and tr_A0A0D9RIF2_A0A0D9RIF2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7E9N0_F7E9N0_MACMU_9544 and tr_A0A2K5MMJ5_A0A2K5MMJ5_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7EIN2_F7EIN2_MACMU_9544 and tr_G7Q2F6_G7Q2F6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7EIP2_F7EIP2_MACMU_9544 and tr_G7Q2F5_G7Q2F5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HCY3_F7HCY3_MACMU_9544 and tr_G7Q2A6_G7Q2A6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HEL8_F7HEL8_MACMU_9544 and tr_G7Q1W3_G7Q1W3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7NYZ0_G7NYZ0_MACFA_9541 and tr_A0A2K6AMH0_A0A2K6AMH0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NMU4_A0A096NMU4_PAPAN_9555 and tr_A0A0D9SAL2_A0A0D9SAL2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NMU4_A0A096NMU4_PAPAN_9555 and tr_A0A2K5LPB7_A0A2K5LPB7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NMU4_A0A096NMU4_PAPAN_9555 and tr_A0A2K5YXC1_A0A2K5YXC1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I4AMF6_A0A2I4AMF6_9TELE_52670 and tr_A0A2I4D5X5_A0A2I4D5X5_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A2K5L712_A0A2K5L712_CERAT_9531 and tr_A0A2K5M267_A0A2K5M267_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2K6ANZ6_A0A2K6ANZ6_MACNE_9545 and tr_A0A2K6BCS6_A0A2K6BCS6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2U4C6N1_A0A2U4C6N1_TURTR_9739 and tr_A0A2U4C6P2_A0A2U4C6P2_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2Y9MBM3_A0A2Y9MBM3_DELLE_9749 and tr_A0A2Y9MZY9_A0A2Y9MZY9_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 50 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/Q96MG7/4_raxmlng_ancestral/Q96MG7.raxml.reduced.phy Alignment comprises 1 partitions and 304 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 304 Gaps: 12.24 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96MG7/4_raxmlng_ancestral/Q96MG7.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/Q96MG7/3_mltree/Q96MG7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 76 / 6080 [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: -153306.169260 [00:00:00 -153306.169260] Initial branch length optimization [00:00:01 -150960.989658] Model parameter optimization (eps = 0.100000) [00:00:27] Tree #1, final logLikelihood: -150635.065665 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.089949,0.250666) (0.142941,0.367973) (0.325826,0.772324) (0.441283,1.525576) 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/Q96MG7/4_raxmlng_ancestral/Q96MG7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96MG7/4_raxmlng_ancestral/Q96MG7.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96MG7/4_raxmlng_ancestral/Q96MG7.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96MG7/4_raxmlng_ancestral/Q96MG7.raxml.log Analysis started: 12-Jul-2021 17:19:23 / finished: 12-Jul-2021 17:19:53 Elapsed time: 29.593 seconds Consumed energy: 2.456 Wh