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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 04-Jun-2021 13:43:57 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16832/2_msa/Q16832_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16832/3_mltree/Q16832.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16832/4_raxmlng_ancestral/Q16832 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803437 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16832/2_msa/Q16832_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 855 sites WARNING: Sequences tr_B4Q8R8_B4Q8R8_DROSI_7240 and tr_B4HWI5_B4HWI5_DROSE_7238 are exactly identical! WARNING: Sequences sp_Q6VNS1_NTRK3_MOUSE_10090 and sp_Q03351_NTRK3_RAT_10116 are exactly identical! WARNING: Sequences sp_Q6VNS1_NTRK3_MOUSE_10090 and tr_A0A1U7QFB5_A0A1U7QFB5_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2J8VWT8_A0A2J8VWT8_PONAB_9601 and tr_A0A2R8MR76_A0A2R8MR76_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2N5B2_H2N5B2_PONAB_9601 and tr_A0A2I3T3D1_A0A2I3T3D1_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2N5B2_H2N5B2_PONAB_9601 and tr_A0A2R9B3Y6_A0A2R9B3Y6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and tr_A0A2J8MRU2_A0A2J8MRU2_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and sp_Q16620_NTRK2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and tr_A0A2R9BIL6_A0A2R9BIL6_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q292H0_Q292H0_DROPS_46245 and tr_B4GDJ7_B4GDJ7_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2RKA1_E2RKA1_CANLF_9615 and tr_G1LBG1_G1LBG1_AILME_9646 are exactly identical! WARNING: Sequences tr_E2RKA1_E2RKA1_CANLF_9615 and tr_M3WAS3_M3WAS3_FELCA_9685 are exactly identical! WARNING: Sequences tr_E2RKA1_E2RKA1_CANLF_9615 and tr_A0A2Y9KA38_A0A2Y9KA38_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3RY88_A0A2I3RY88_PANTR_9598 and tr_A0A2R8ZRG9_A0A2R8ZRG9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3T8J4_A0A2I3T8J4_PANTR_9598 and sp_Q5IS37_NTRK3_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3T8J4_A0A2I3T8J4_PANTR_9598 and tr_A0A2R9CFJ3_A0A2R9CFJ3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TDE7_A0A2I3TDE7_PANTR_9598 and tr_A0A2R8ZYT3_A0A2R8ZYT3_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7FCZ2_F7FCZ2_MONDO_13616 and tr_G3WY32_G3WY32_SARHA_9305 are exactly identical! WARNING: Sequences tr_A0A1D5Q156_A0A1D5Q156_MACMU_9544 and tr_A0A096MUC1_A0A096MUC1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5RHZ9_A0A1D5RHZ9_MACMU_9544 and tr_A0A2K5LTN5_A0A2K5LTN5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5RHZ9_A0A1D5RHZ9_MACMU_9544 and tr_A0A2K6CF21_A0A2K6CF21_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BW77_F7BW77_MACMU_9544 and tr_A0A0D9R7H0_A0A0D9R7H0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7BW77_F7BW77_MACMU_9544 and tr_A0A2K6D281_A0A2K6D281_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DGW1_F7DGW1_MACMU_9544 and tr_G7PSM1_G7PSM1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7DGW1_F7DGW1_MACMU_9544 and tr_A0A2I3MH64_A0A2I3MH64_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DGW1_F7DGW1_MACMU_9544 and tr_A0A2K6BIB6_A0A2K6BIB6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DJ75_F7DJ75_MACMU_9544 and tr_A0A2K5NXD9_A0A2K5NXD9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DJ75_F7DJ75_MACMU_9544 and tr_A0A2K6E1K6_A0A2K6E1K6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DJ75_F7DJ75_MACMU_9544 and tr_A0A2K5ZMQ5_A0A2K5ZMQ5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HFZ8_F7HFZ8_MACMU_9544 and tr_A0A096P0W8_A0A096P0W8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F4WGV1_F4WGV1_ACREC_103372 and tr_A0A195FPJ8_A0A195FPJ8_9HYME_34720 are exactly identical! WARNING: Sequences tr_G7P9D5_G7P9D5_MACFA_9541 and tr_A0A2K5Y8E4_A0A2K5Y8E4_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3WLP2_M3WLP2_FELCA_9685 and tr_A0A2U3VSS0_A0A2U3VSS0_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A0V1CN21_A0A0V1CN21_TRIBR_45882 and tr_A0A0V0X2J3_A0A0V0X2J3_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CN21_A0A0V1CN21_TRIBR_45882 and tr_A0A0V1L3W9_A0A0V1L3W9_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CN21_A0A0V1CN21_TRIBR_45882 and tr_A0A0V0UA62_A0A0V0UA62_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1D0K0_A0A0V1D0K0_TRIBR_45882 and tr_A0A0V1P316_A0A0V1P316_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1D0K0_A0A0V1D0K0_TRIBR_45882 and tr_A0A0V0TH33_A0A0V0TH33_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A226NHF2_A0A226NHF2_CALSU_9009 and tr_A0A226PQ01_A0A226PQ01_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0R3Z4_A0A2D0R3Z4_ICTPU_7998 and tr_A0A2D0R414_A0A2D0R414_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R3Z4_A0A2D0R3Z4_ICTPU_7998 and tr_A0A2D0R4R8_A0A2D0R4R8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5L1F0_A0A2K5L1F0_CERAT_9531 and tr_A0A2K6AMP9_A0A2K6AMP9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2U4BS11_A0A2U4BS11_TURTR_9739 and tr_A0A2Y9MAX3_A0A2Y9MAX3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BS11_A0A2U4BS11_TURTR_9739 and tr_A0A383ZPG7_A0A383ZPG7_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 44 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16832/4_raxmlng_ancestral/Q16832.raxml.reduced.phy Alignment comprises 1 partitions and 855 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 855 Gaps: 33.17 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16832/4_raxmlng_ancestral/Q16832.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16832/3_mltree/Q16832.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 214 / 17120 [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: -280652.645454 [00:00:00 -280652.645454] Initial branch length optimization [00:00:02 -267273.684358] Model parameter optimization (eps = 0.100000) [00:01:13] Tree #1, final logLikelihood: -266443.264077 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.127943,0.369034) (0.136314,0.444988) (0.427005,0.834557) (0.308737,1.735348) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16832/4_raxmlng_ancestral/Q16832.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16832/4_raxmlng_ancestral/Q16832.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16832/4_raxmlng_ancestral/Q16832.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q16832/4_raxmlng_ancestral/Q16832.raxml.log Analysis started: 04-Jun-2021 13:43:57 / finished: 04-Jun-2021 13:45:18 Elapsed time: 81.017 seconds