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 02:27:24 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07225/2_msa/P07225_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07225/3_mltree/P07225.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07225/4_raxmlng_ancestral/P07225 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622676444 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/P07225/2_msa/P07225_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 676 sites WARNING: Sequences tr_A0A1D5P380_A0A1D5P380_CHICK_9031 and tr_R0LJA8_R0LJA8_ANAPL_8839 are exactly identical! WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_A0A2J8XCL5_A0A2J8XCL5_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_H2REY4_H2REY4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and sp_Q12805_FBLN3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_G7NA36_G7NA36_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_A0A096NP06_A0A096NP06_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_A0A0D9RPF4_A0A0D9RPF4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_A0A2K5KXY1_A0A2K5KXY1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_A0A2K6DZ29_A0A2K6DZ29_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RE04_G1RE04_NOMLE_61853 and tr_A0A2K5YW69_A0A2K5YW69_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3S458_G3S458_GORGO_9595 and tr_H2QGC8_H2QGC8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S458_G3S458_GORGO_9595 and tr_A0A2R9A9D5_A0A2R9A9D5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1K2D7_G1K2D7_CANLF_9615 and sp_P19540_FA9_CANLF_9615 are exactly identical! WARNING: Sequences tr_H2Q7T9_H2Q7T9_PANTR_9598 and sp_P00742_FA10_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q7T9_H2Q7T9_PANTR_9598 and tr_A0A2R9B696_A0A2R9B696_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q95ND7_FA9_PANTR_9598 and sp_P00740_FA9_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_G7PBA1_G7PBA1_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_A0A096NM08_A0A096NM08_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_A0A2K5L3Z1_A0A2K5L3Z1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_A0A2K6BW09_A0A2K6BW09_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6SB17_F6SB17_MACMU_9544 and tr_G7PVR8_G7PVR8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GHR4_F7GHR4_MACMU_9544 and tr_G7Q1U2_G7Q1U2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GHR4_F7GHR4_MACMU_9544 and tr_A0A2K6ARW6_A0A2K6ARW6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GHR4_F7GHR4_MACMU_9544 and tr_A0A2K5XMF6_A0A2K5XMF6_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7H9U3_F7H9U3_MACMU_9544 and tr_A0A0D9QUL2_A0A0D9QUL2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7H9U3_F7H9U3_MACMU_9544 and tr_A0A2K5L0F9_A0A2K5L0F9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7H9U3_F7H9U3_MACMU_9544 and tr_A0A2K6A267_A0A2K6A267_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A140T851_A0A140T851_BOVIN_9913 and sp_P00745_PROC_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3VVE6_M3VVE6_FELCA_9685 and tr_A0A2U3W686_A0A2U3W686_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A096NEF0_A0A096NEF0_PAPAN_9555 and tr_A0A2K5KMW6_A0A2K5KMW6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MQ48_A0A2I3MQ48_PAPAN_9555 and tr_A0A2K5LFG6_A0A2K5LFG6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A9X172_A9X172_PAPAN_9555 and tr_A0A2K5NQ25_A0A2K5NQ25_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091UNZ6_A0A091UNZ6_NIPNI_128390 and tr_A0A087RJQ8_A0A087RJQ8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UNZ6_A0A091UNZ6_NIPNI_128390 and tr_A0A091VRV3_A0A091VRV3_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A0V0X293_A0A0V0X293_9BILA_92179 and tr_A0A0V1L600_A0A0V1L600_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0UQZ3_A0A0V0UQZ3_9BILA_181606 and tr_A0A0V1P4F3_A0A0V1P4F3_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0UQZ3_A0A0V0UQZ3_9BILA_181606 and tr_A0A0V0TJX0_A0A0V0TJX0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A2D0RV45_A0A2D0RV45_ICTPU_7998 and tr_A0A2D0RV53_A0A2D0RV53_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RV45_A0A2D0RV45_ICTPU_7998 and tr_A0A2D0RV58_A0A2D0RV58_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RV45_A0A2D0RV45_ICTPU_7998 and tr_A0A2D0RW13_A0A2D0RW13_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RV45_A0A2D0RV45_ICTPU_7998 and tr_A0A2D0RWP6_A0A2D0RWP6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4BY46_A0A2U4BY46_TURTR_9739 and tr_A0A2Y9Q5P9_A0A2Y9Q5P9_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 42 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/P07225/4_raxmlng_ancestral/P07225.raxml.reduced.phy Alignment comprises 1 partitions and 676 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 676 Gaps: 44.61 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07225/4_raxmlng_ancestral/P07225.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/P07225/3_mltree/P07225.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 169 / 13520 [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: -237345.134207 [00:00:00 -237345.134207] Initial branch length optimization [00:00:01 -235667.488436] Model parameter optimization (eps = 0.100000) [00:00:39] Tree #1, final logLikelihood: -234798.413783 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.096209,0.212425) (0.055694,1.558910) (0.519246,0.790236) (0.328851,1.466968) 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/P07225/4_raxmlng_ancestral/P07225.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07225/4_raxmlng_ancestral/P07225.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07225/4_raxmlng_ancestral/P07225.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07225/4_raxmlng_ancestral/P07225.raxml.log Analysis started: 03-Jun-2021 02:27:24 / finished: 03-Jun-2021 02:28:10 Elapsed time: 45.237 seconds Consumed energy: 2.667 Wh