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 17:43:52 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96N96/2_msa/Q96N96_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96N96/3_mltree/Q96N96.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96N96/4_raxmlng_ancestral/Q96N96 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101032 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/Q96N96/2_msa/Q96N96_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 652 sites WARNING: Sequences tr_A0A2R8QHV5_A0A2R8QHV5_DANRE_7955 and tr_A0A2R8QRI5_A0A2R8QRI5_DANRE_7955 are exactly identical! WARNING: Sequences tr_A0A2I2ZML1_A0A2I2ZML1_GORGO_9595 and sp_Q9H7P9_PKHG2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RRP5_G3RRP5_GORGO_9595 and tr_H2PQI3_H2PQI3_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RRP5_G3RRP5_GORGO_9595 and tr_A0A2I3SC96_A0A2I3SC96_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RRP5_G3RRP5_GORGO_9595 and sp_Q70Z35_PREX2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TQA2_A0A2I3TQA2_PANTR_9598 and tr_A0A2R8ZLA9_A0A2R8ZLA9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R6W0_H2R6W0_PANTR_9598 and sp_Q9ULL1_PKHG1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R6W0_H2R6W0_PANTR_9598 and tr_A0A2R9BZW5_A0A2R9BZW5_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7BJ16_K7BJ16_PANTR_9598 and tr_A0A2R9BI86_A0A2R9BI86_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7DVN5_F7DVN5_HORSE_9796 and tr_G1L052_G1L052_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A158P3R1_A0A158P3R1_ATTCE_12957 and tr_F4X211_F4X211_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158P3R1_A0A158P3R1_ATTCE_12957 and tr_A0A195BCT4_A0A195BCT4_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158P3R1_A0A158P3R1_ATTCE_12957 and tr_A0A195F086_A0A195F086_9HYME_34720 are exactly identical! WARNING: Sequences tr_F6WVV6_F6WVV6_MACMU_9544 and tr_A0A2K6E6G3_A0A2K6E6G3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7G8P7_F7G8P7_MACMU_9544 and tr_A0A2K5MUX2_A0A2K5MUX2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PBZ7_G7PBZ7_MACFA_9541 and tr_A0A096MWT3_A0A096MWT3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PBZ7_G7PBZ7_MACFA_9541 and tr_A0A2K5KK59_A0A2K5KK59_CERAT_9531 are exactly identical! WARNING: Sequences tr_U3JRY0_U3JRY0_FICAL_59894 and tr_A0A218VC28_A0A218VC28_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A2I3LP44_A0A2I3LP44_PAPAN_9555 and tr_A0A2K5NIF0_A0A2K5NIF0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LP44_A0A2I3LP44_PAPAN_9555 and tr_A0A2K6AMZ0_A0A2K6AMZ0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3LP44_A0A2I3LP44_PAPAN_9555 and tr_A0A2K5XW67_A0A2K5XW67_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091X471_A0A091X471_NIPNI_128390 and tr_A0A087QQS5_A0A087QQS5_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091X471_A0A091X471_NIPNI_128390 and tr_A0A091H1D7_A0A091H1D7_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091X471_A0A091X471_NIPNI_128390 and tr_A0A0A0AJ58_A0A0A0AJ58_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091X471_A0A091X471_NIPNI_128390 and tr_A0A093GAT2_A0A093GAT2_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A1S3IUH0_A0A1S3IUH0_LINUN_7574 and tr_A0A1S3IUH3_A0A1S3IUH3_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3IUH0_A0A1S3IUH0_LINUN_7574 and tr_A0A1S3IUH5_A0A1S3IUH5_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3IUH0_A0A1S3IUH0_LINUN_7574 and tr_A0A1S3IUV9_A0A1S3IUV9_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3IUH0_A0A1S3IUH0_LINUN_7574 and tr_A0A1S3IUW4_A0A1S3IUW4_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3IUH0_A0A1S3IUH0_LINUN_7574 and tr_A0A1S3IWD2_A0A1S3IWD2_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A2D0PYG6_A0A2D0PYG6_ICTPU_7998 and tr_A0A2D0Q127_A0A2D0Q127_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0Q9N4_A0A2D0Q9N4_ICTPU_7998 and tr_W5UB82_W5UB82_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R9E4_A0A2D0R9E4_ICTPU_7998 and tr_A0A2D0RAL6_A0A2D0RAL6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SST6_A0A2D0SST6_ICTPU_7998 and tr_A0A2D0STC4_A0A2D0STC4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T6X3_A0A2D0T6X3_ICTPU_7998 and tr_A0A2D0T7M4_A0A2D0T7M4_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 35 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/Q96N96/4_raxmlng_ancestral/Q96N96.raxml.reduced.phy Alignment comprises 1 partitions and 652 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 652 Gaps: 32.32 % Invariant sites: 0.15 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96N96/4_raxmlng_ancestral/Q96N96.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/Q96N96/3_mltree/Q96N96.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 163 / 13040 [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: -206937.422211 [00:00:00 -206937.422211] Initial branch length optimization [00:00:01 -196174.443447] Model parameter optimization (eps = 0.100000) [00:00:47] Tree #1, final logLikelihood: -195713.253562 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.106109,0.410570) (0.083247,0.487407) (0.378427,0.697868) (0.432217,1.507965) 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/Q96N96/4_raxmlng_ancestral/Q96N96.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96N96/4_raxmlng_ancestral/Q96N96.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96N96/4_raxmlng_ancestral/Q96N96.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96N96/4_raxmlng_ancestral/Q96N96.raxml.log Analysis started: 12-Jul-2021 17:43:52 / finished: 12-Jul-2021 17:44:45 Elapsed time: 53.764 seconds Consumed energy: 4.504 Wh