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 16:39:17 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JH8/2_msa/Q96JH8_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JH8/3_mltree/Q96JH8.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JH8/4_raxmlng_ancestral/Q96JH8 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626097157 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/Q96JH8/2_msa/Q96JH8_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1075 sites WARNING: Sequences tr_G1QMJ5_G1QMJ5_NOMLE_61853 and tr_G3QWN1_G3QWN1_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QMJ5_G1QMJ5_NOMLE_61853 and tr_K7DKX9_K7DKX9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QMJ5_G1QMJ5_NOMLE_61853 and sp_P57105_SYJ2B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QMJ5_G1QMJ5_NOMLE_61853 and tr_A0A2R8ZAC0_A0A2R8ZAC0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZL88_A0A2I2ZL88_GORGO_9595 and sp_Q96QZ7_MAGI1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QFY4_G3QFY4_GORGO_9595 and tr_H2QGS3_H2QGS3_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A158NM77_A0A158NM77_ATTCE_12957 and tr_A0A195BWZ5_A0A195BWZ5_9HYME_520822 are exactly identical! WARNING: Sequences sp_Q12923_PTN13_HUMAN_9606 and tr_A0A2R9BND5_A0A2R9BND5_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6V3H6_F6V3H6_MACMU_9544 and tr_A0A096NG20_A0A096NG20_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6V3H6_F6V3H6_MACMU_9544 and tr_A0A2K5LC48_A0A2K5LC48_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6V3H6_F6V3H6_MACMU_9544 and tr_A0A2K6BVS0_A0A2K6BVS0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6V3H6_F6V3H6_MACMU_9544 and tr_A0A2K5Z3N5_A0A2K5Z3N5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7P1X6_G7P1X6_MACFA_9541 and tr_A0A2K5YU87_A0A2K5YU87_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0ADL1_A0A0A0ADL1_CHAVO_50402 and tr_A0A091HYN7_A0A091HYN7_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A226NKY7_A0A226NKY7_CALSU_9009 and tr_A0A226PFM1_A0A226PFM1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PQ69_A0A2D0PQ69_ICTPU_7998 and tr_A0A2D0PR72_A0A2D0PR72_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QYS8_A0A2D0QYS8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R0K1_A0A2D0R0K1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R1A2_A0A2D0R1A2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYT2_A0A2D0QYT2_ICTPU_7998 and tr_A0A2D0QZ23_A0A2D0QZ23_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYT3_A0A2D0QYT3_ICTPU_7998 and tr_A0A2D0QZ12_A0A2D0QZ12_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYT3_A0A2D0QYT3_ICTPU_7998 and tr_A0A2D0QZ17_A0A2D0QZ17_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYT3_A0A2D0QYT3_ICTPU_7998 and tr_A0A2D0R0L3_A0A2D0R0L3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYT3_A0A2D0QYT3_ICTPU_7998 and tr_A0A2D0R1B5_A0A2D0R1B5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RZG4_A0A2D0RZG4_ICTPU_7998 and tr_A0A2D0RZH2_A0A2D0RZH2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RZH3_A0A2D0RZH3_ICTPU_7998 and tr_A0A2D0S108_A0A2D0S108_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SBX9_A0A2D0SBX9_ICTPU_7998 and tr_A0A2D0SCJ8_A0A2D0SCJ8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KLD2_A0A2K5KLD2_CERAT_9531 and tr_A0A2K6E3X2_A0A2K6E3X2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5N7G5_A0A2K5N7G5_CERAT_9531 and tr_A0A2K6CCH0_A0A2K6CCH0_MACNE_9545 are exactly identical! WARNING: Duplicate sequences found: 29 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/Q96JH8/4_raxmlng_ancestral/Q96JH8.raxml.reduced.phy Alignment comprises 1 partitions and 1075 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1075 Gaps: 50.66 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JH8/4_raxmlng_ancestral/Q96JH8.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/Q96JH8/3_mltree/Q96JH8.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 269 / 21520 [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: -289104.312224 [00:00:00 -289104.312224] Initial branch length optimization [00:00:02 -286265.131750] Model parameter optimization (eps = 0.100000) 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 12-Jul-2021 18:16:27 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JH8/2_msa/Q96JH8_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JH8/3_mltree/Q96JH8.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JH8/4_raxmlng_ancestral/Q96JH8 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102987 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 WARNING: The model you specified on the command line (LG4X) will be ignored since the binary MSA file already contains a model definition. If you want to change the model, please re-run RAxML-NG with the original PHYLIP/FASTA alignment and --redo option. [00:00:00] Loading binary alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JH8/4_raxmlng_ancestral/Q96JH8.raxml.rba [00:00:00] Alignment comprises 1001 taxa, 1 partitions and 1075 patterns Partition 0: noname Model: LG4X+R4 Alignment sites: 1075 Gaps: 50.66 % Invariant sites: 0.00 % Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] NOTE: Resuming execution from checkpoint (logLH: -286265.13, ML trees: 0, bootstraps: 0) [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 269 / 21520 [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: -286265.131750 [00:00:00 -286265.131750] Model parameter optimization (eps = 0.100000) [00:01:10] Tree #1, final logLikelihood: -285020.145255 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.133504,0.723430) (0.035934,0.357975) (0.370506,0.685383) (0.460056,1.383782) 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/Q96JH8/4_raxmlng_ancestral/Q96JH8.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JH8/4_raxmlng_ancestral/Q96JH8.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JH8/4_raxmlng_ancestral/Q96JH8.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JH8/4_raxmlng_ancestral/Q96JH8.raxml.log Analysis started: 12-Jul-2021 18:16:27 / finished: 12-Jul-2021 18:17:48 Elapsed time: 80.818 seconds (this run) / 83.225 seconds (total with restarts) Consumed energy: 4.489 Wh