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 03:18:38 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60733/2_msa/O60733_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60733/3_mltree/O60733.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60733/4_raxmlng_ancestral/O60733 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622679518 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/O60733/2_msa/O60733_nogap_msa.fasta [00:00:00] Loaded alignment with 998 taxa and 806 sites WARNING: Sequences sp_Q8VBX0_ASB13_MOUSE_10090 and tr_G3GR75_G3GR75_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q8VBX0_ASB13_MOUSE_10090 and tr_A0A1U7QYQ7_A0A1U7QYQ7_MESAU_10036 are exactly identical! WARNING: Sequences tr_G1RKW4_G1RKW4_NOMLE_61853 and tr_F7BPA7_F7BPA7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RKW4_G1RKW4_NOMLE_61853 and tr_G7PE51_G7PE51_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RKW4_G1RKW4_NOMLE_61853 and tr_A0A0D9RMI4_A0A0D9RMI4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RKW4_G1RKW4_NOMLE_61853 and tr_A0A2K6CVV0_A0A2K6CVV0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_G3S4C5_G3S4C5_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_H2R3U2_H2R3U2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and sp_Q01484_ANK2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_F7H4E0_F7H4E0_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_G7P649_G7P649_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_A0A096N0E1_A0A096N0E1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_A0A0D9QUX9_A0A0D9QUX9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_A0A2K5MCB6_A0A2K5MCB6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_A0A2K5YPQ5_A0A2K5YPQ5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S2U2_G1S2U2_NOMLE_61853 and tr_A0A2R9BUB3_A0A2R9BUB3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QDY4_G3QDY4_GORGO_9595 and tr_H2N9N8_H2N9N8_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QDY4_G3QDY4_GORGO_9595 and tr_H2R1U5_H2R1U5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QDY4_G3QDY4_GORGO_9595 and sp_Q8WXK3_ASB13_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QDY4_G3QDY4_GORGO_9595 and tr_A0A1S3ELA0_A0A1S3ELA0_DIPOR_10020 are exactly identical! WARNING: Sequences tr_F1P6P1_F1P6P1_CANLF_9615 and tr_A0A287AUI5_A0A287AUI5_PIG_9823 are exactly identical! WARNING: Sequences tr_F1P6P1_F1P6P1_CANLF_9615 and tr_A0A337SR04_A0A337SR04_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1P6P1_F1P6P1_CANLF_9615 and tr_A0A2U3WE70_A0A2U3WE70_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1P6P1_F1P6P1_CANLF_9615 and tr_A0A384BYK5_A0A384BYK5_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3TDL6_A0A2I3TDL6_PANTR_9598 and tr_A0A2R8ZRW6_A0A2R8ZRW6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TN78_A0A2I3TN78_PANTR_9598 and tr_A0A2R9AU58_A0A2R9AU58_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R3M2_H2R3M2_PANTR_9598 and sp_P16157_ANK1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R3M2_H2R3M2_PANTR_9598 and tr_A0A0D9RRD4_A0A0D9RRD4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2R3M2_H2R3M2_PANTR_9598 and tr_A0A2R9AEU3_A0A2R9AEU3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A087ZSA8_A0A087ZSA8_APIME_7460 and tr_A0A2A3ENU8_A0A2A3ENU8_APICC_94128 are exactly identical! WARNING: Sequences tr_F7EV70_F7EV70_MACMU_9544 and tr_G7P080_G7P080_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7EV70_F7EV70_MACMU_9544 and tr_A0A0D9R792_A0A0D9R792_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7EV70_F7EV70_MACMU_9544 and tr_A0A2K6B1S8_A0A2K6B1S8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7EV70_F7EV70_MACMU_9544 and tr_A0A2K5XP67_A0A2K5XP67_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3TDC5_G3TDC5_LOXAF_9785 and tr_A0A2Y9DSK4_A0A2Y9DSK4_TRIMA_127582 are exactly identical! WARNING: Sequences tr_F4WT31_F4WT31_ACREC_103372 and tr_A0A195F701_A0A195F701_9HYME_34720 are exactly identical! WARNING: Sequences tr_B4MF25_B4MF25_DROVI_7244 and tr_D0Z7C6_D0Z7C6_DROVI_7244 are exactly identical! WARNING: Sequences tr_G7PBR2_G7PBR2_MACFA_9541 and tr_A0A2K5MAP3_A0A2K5MAP3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A078I827_A0A078I827_BRANA_3708 and tr_A0A0D3E7P7_A0A0D3E7P7_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0V0S5A0_A0A0V0S5A0_9BILA_6336 and tr_A0A0V0WNA2_A0A0V0WNA2_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0S5A0_A0A0V0S5A0_9BILA_6336 and tr_A0A0V1LCQ3_A0A0V1LCQ3_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0S5A0_A0A0V0S5A0_9BILA_6336 and tr_A0A0V0ZB57_A0A0V0ZB57_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1D676_A0A0V1D676_TRIBR_45882 and tr_A0A0V0VBE4_A0A0V0VBE4_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D676_A0A0V1D676_TRIBR_45882 and tr_A0A0V1P299_A0A0V1P299_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1D676_A0A0V1D676_TRIBR_45882 and tr_A0A0V0UDW4_A0A0V0UDW4_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A226NKX9_A0A226NKX9_CALSU_9009 and tr_A0A226PXS3_A0A226PXS3_COLVI_9014 are exactly identical! WARNING: Duplicate sequences found: 46 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/O60733/4_raxmlng_ancestral/O60733.raxml.reduced.phy Alignment comprises 1 partitions and 806 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 806 Gaps: 42.42 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60733/4_raxmlng_ancestral/O60733.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/O60733/3_mltree/O60733.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 202 / 16160 [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: -317658.076694 [00:00:00 -317658.076694] Initial branch length optimization [00:00:01 -315261.618015] Model parameter optimization (eps = 0.100000) [00:01:10] Tree #1, final logLikelihood: -313836.877159 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.109574,0.463868) (0.126612,0.479799) (0.425484,0.876511) (0.338330,1.523608) 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/O60733/4_raxmlng_ancestral/O60733.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60733/4_raxmlng_ancestral/O60733.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60733/4_raxmlng_ancestral/O60733.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60733/4_raxmlng_ancestral/O60733.raxml.log Analysis started: 03-Jun-2021 03:18:38 / finished: 03-Jun-2021 03:19:59 Elapsed time: 80.351 seconds Consumed energy: 6.292 Wh