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 02:45:23 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42336/2_msa/P42336_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42336/3_mltree/P42336.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42336/4_raxmlng_ancestral/P42336 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677523 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/P42336/2_msa/P42336_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1068 sites WARNING: Sequences tr_M3Z0I7_M3Z0I7_MUSPF_9669 and tr_F1Q3M8_F1Q3M8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z0I7_M3Z0I7_MUSPF_9669 and tr_F6VFI8_F6VFI8_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3Z0I7_M3Z0I7_MUSPF_9669 and tr_W5QHQ9_W5QHQ9_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3Z0I7_M3Z0I7_MUSPF_9669 and tr_G1LW99_G1LW99_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z0I7_M3Z0I7_MUSPF_9669 and sp_P32871_PK3CA_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3Z0I7_M3Z0I7_MUSPF_9669 and tr_M3WP72_M3WP72_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z0I7_M3Z0I7_MUSPF_9669 and tr_A0A2U3VSW6_A0A2U3VSW6_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z0I7_M3Z0I7_MUSPF_9669 and tr_A0A2U3YQH7_A0A2U3YQH7_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Z0I7_M3Z0I7_MUSPF_9669 and tr_A0A2Y9JE77_A0A2Y9JE77_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z0I7_M3Z0I7_MUSPF_9669 and tr_A0A2Y9MZW2_A0A2Y9MZW2_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3Z0I7_M3Z0I7_MUSPF_9669 and tr_A0A2Y9F7B3_A0A2Y9F7B3_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G3R1S6_G3R1S6_GORGO_9595 and sp_P42336_PK3CA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R1S6_G3R1S6_GORGO_9595 and tr_H9FVU5_H9FVU5_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3R1S6_G3R1S6_GORGO_9595 and tr_G7NZ32_G7NZ32_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3R1S6_G3R1S6_GORGO_9595 and tr_A0A096MY63_A0A096MY63_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3R1S6_G3R1S6_GORGO_9595 and tr_A0A0D9RKI4_A0A0D9RKI4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3R1S6_G3R1S6_GORGO_9595 and tr_A0A2K6C9I6_A0A2K6C9I6_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3R1S6_G3R1S6_GORGO_9595 and tr_A0A2K5YVM5_A0A2K5YVM5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3S7D1_G3S7D1_GORGO_9595 and tr_A0A2R9CFV4_A0A2R9CFV4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QNG6_H2QNG6_PANTR_9598 and tr_A0A2R9AJ46_A0A2R9AJ46_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NHH3_A0A158NHH3_ATTCE_12957 and tr_A0A195AV33_A0A195AV33_9HYME_520822 are exactly identical! WARNING: Sequences tr_F6W7C8_F6W7C8_MACMU_9544 and tr_G7P2F4_G7P2F4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6W7C8_F6W7C8_MACMU_9544 and tr_A0A096NGU7_A0A096NGU7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6W7C8_F6W7C8_MACMU_9544 and tr_A0A2K5NAR6_A0A2K5NAR6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6W7C8_F6W7C8_MACMU_9544 and tr_A0A2K6DNW0_A0A2K6DNW0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7F3S0_F7F3S0_MACMU_9544 and tr_G7P030_G7P030_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7F3S0_F7F3S0_MACMU_9544 and tr_A0A0D9RFE7_A0A0D9RFE7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H9ESL7_H9ESL7_MACMU_9544 and tr_A0A2K6E5P9_A0A2K6E5P9_MACNE_9545 are exactly identical! WARNING: Sequences tr_U3DZL6_U3DZL6_CALJA_9483 and tr_I3LMG0_I3LMG0_PIG_9823 are exactly identical! WARNING: Sequences tr_G7PQM7_G7PQM7_MACFA_9541 and tr_A0A2K5KPN9_A0A2K5KPN9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PQM7_G7PQM7_MACFA_9541 and tr_A0A2K6BX54_A0A2K6BX54_MACNE_9545 are exactly identical! WARNING: Sequences tr_U3IZV1_U3IZV1_ANAPL_8839 and tr_A0A091WH84_A0A091WH84_OPIHO_30419 are exactly identical! WARNING: Sequences tr_U3IZV1_U3IZV1_ANAPL_8839 and tr_A0A0A0A465_A0A0A0A465_CHAVO_50402 are exactly identical! WARNING: Sequences tr_W2R1M9_W2R1M9_PHYPN_761204 and tr_A0A0W8C749_A0A0W8C749_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A2I3MD87_A0A2I3MD87_PAPAN_9555 and tr_A0A2K5MGC2_A0A2K5MGC2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0V1CMA1_A0A0V1CMA1_TRIBR_45882 and tr_A0A0V1P1N7_A0A0V1P1N7_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S3LVG7_A0A1S3LVG7_SALSA_8030 and tr_A0A060VNB5_A0A060VNB5_ONCMY_8022 are exactly identical! WARNING: Duplicate sequences found: 37 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/P42336/4_raxmlng_ancestral/P42336.raxml.reduced.phy Alignment comprises 1 partitions and 1068 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1068 Gaps: 17.28 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42336/4_raxmlng_ancestral/P42336.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/P42336/3_mltree/P42336.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 267 / 21360 [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: -420034.642919 [00:00:00 -420034.642919] Initial branch length optimization [00:00:02 -419005.795126] Model parameter optimization (eps = 0.100000) [00:00:44] Tree #1, final logLikelihood: -418346.579983 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.115359,0.287786) (0.175017,0.417317) (0.341275,0.834701) (0.368350,1.653053) 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/P42336/4_raxmlng_ancestral/P42336.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42336/4_raxmlng_ancestral/P42336.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42336/4_raxmlng_ancestral/P42336.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P42336/4_raxmlng_ancestral/P42336.raxml.log Analysis started: 03-Jun-2021 02:45:23 / finished: 03-Jun-2021 02:46:17 Elapsed time: 53.682 seconds Consumed energy: 3.913 Wh