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 03-Jun-2021 02:14:14 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56715/2_msa/P56715_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56715/3_mltree/P56715.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56715/4_raxmlng_ancestral/P56715 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622675654 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/P56715/2_msa/P56715_nogap_msa.fasta [00:00:00] Loaded alignment with 683 taxa and 2156 sites WARNING: Sequences tr_Q98SS5_Q98SS5_CHICK_9031 and tr_U3K952_U3K952_FICAL_59894 are exactly identical! WARNING: Sequences tr_Q98SS5_Q98SS5_CHICK_9031 and tr_A0A218UTP0_A0A218UTP0_9PASE_299123 are exactly identical! WARNING: Sequences sp_O88809_DCX_MOUSE_10090 and tr_G1SS88_G1SS88_RABIT_9986 are exactly identical! WARNING: Sequences sp_O88809_DCX_MOUSE_10090 and tr_H0UUE2_H0UUE2_CAVPO_10141 are exactly identical! WARNING: Sequences sp_O88809_DCX_MOUSE_10090 and sp_O43602_DCX_HUMAN_9606 are exactly identical! WARNING: Sequences sp_O88809_DCX_MOUSE_10090 and tr_G3SWI5_G3SWI5_LOXAF_9785 are exactly identical! WARNING: Sequences sp_O88809_DCX_MOUSE_10090 and tr_A0A2R8P214_A0A2R8P214_CALJA_9483 are exactly identical! WARNING: Sequences sp_O88809_DCX_MOUSE_10090 and tr_A0A2U3VWN3_A0A2U3VWN3_ODORO_9708 are exactly identical! WARNING: Sequences sp_O88809_DCX_MOUSE_10090 and tr_A0A2Y9L2F4_A0A2Y9L2F4_ENHLU_391180 are exactly identical! WARNING: Sequences sp_O88809_DCX_MOUSE_10090 and tr_A0A2Y9LZH7_A0A2Y9LZH7_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3XY62_M3XY62_MUSPF_9669 and tr_F7AM16_F7AM16_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3XY62_M3XY62_MUSPF_9669 and tr_K7GL04_K7GL04_PIG_9823 are exactly identical! WARNING: Sequences tr_M3XY62_M3XY62_MUSPF_9669 and tr_M3W315_M3W315_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2I3GFE3_A0A2I3GFE3_NOMLE_61853 and tr_A0A2I2Y344_A0A2I2Y344_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GFE3_A0A2I3GFE3_NOMLE_61853 and tr_A0A2I3T205_A0A2I3T205_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GFE3_A0A2I3GFE3_NOMLE_61853 and sp_O15075_DCLK1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GFE3_A0A2I3GFE3_NOMLE_61853 and tr_F7CZB2_F7CZB2_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GFE3_A0A2I3GFE3_NOMLE_61853 and tr_F6U0W2_F6U0W2_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3GFE3_A0A2I3GFE3_NOMLE_61853 and tr_G1LDC0_G1LDC0_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A2I3GFE3_A0A2I3GFE3_NOMLE_61853 and tr_G7PW04_G7PW04_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3GFE3_A0A2I3GFE3_NOMLE_61853 and tr_A0A2K5KQA6_A0A2K5KQA6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GFE3_A0A2I3GFE3_NOMLE_61853 and tr_A0A2K6BAQ9_A0A2K6BAQ9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GFE3_A0A2I3GFE3_NOMLE_61853 and tr_A0A2K6ABE0_A0A2K6ABE0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3GFE3_A0A2I3GFE3_NOMLE_61853 and tr_A0A2R9BKT5_A0A2R9BKT5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3GFE3_A0A2I3GFE3_NOMLE_61853 and tr_A0A2Y9KQV2_A0A2Y9KQV2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I2Z3G2_A0A2I2Z3G2_GORGO_9595 and tr_A0A2I3RS55_A0A2I3RS55_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Z3G2_A0A2I2Z3G2_GORGO_9595 and tr_A0A2R9B5W7_A0A2R9B5W7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RDR8_G3RDR8_GORGO_9595 and tr_A0A2I3SSW0_A0A2I3SSW0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RDR8_G3RDR8_GORGO_9595 and tr_A0A2R9CEE0_A0A2R9CEE0_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PWI1_H2PWI1_PONAB_9601 and tr_H0XQB5_H0XQB5_OTOGA_30611 are exactly identical! WARNING: Sequences tr_H2PWI1_H2PWI1_PONAB_9601 and tr_G1LZZ6_G1LZZ6_AILME_9646 are exactly identical! WARNING: Sequences tr_H2PWI1_H2PWI1_PONAB_9601 and tr_G7Q3H3_G7Q3H3_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2PWI1_H2PWI1_PONAB_9601 and tr_A0A3Q0EIL6_A0A3Q0EIL6_TARSY_1868482 are exactly identical! WARNING: Sequences tr_H2PWI1_H2PWI1_PONAB_9601 and tr_A0A2Y9DRS1_A0A2Y9DRS1_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H2PWI1_H2PWI1_PONAB_9601 and tr_A0A2Y9EPT7_A0A2Y9EPT7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_H2PWI1_H2PWI1_PONAB_9601 and tr_A0A384DL61_A0A384DL61_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A0R3RE91_A0A0R3RE91_BRUMA_6279 and tr_A0A0R3Q304_A0A0R3Q304_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A158N8S7_A0A158N8S7_ONCVO_6282 and tr_A0A182E563_A0A182E563_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A2I3MBC5_A0A2I3MBC5_PAPAN_9555 and tr_A0A2K6BJB6_A0A2K6BJB6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3MBC5_A0A2I3MBC5_PAPAN_9555 and tr_A0A2K5XBF7_A0A2K5XBF7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091IR99_A0A091IR99_EGRGA_188379 and tr_A0A091UYA1_A0A091UYA1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IR99_A0A091IR99_EGRGA_188379 and tr_A0A091GIW9_A0A091GIW9_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091IVJ2_A0A091IVJ2_EGRGA_188379 and tr_A0A093PPH8_A0A093PPH8_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091IVJ2_A0A091IVJ2_EGRGA_188379 and tr_A0A087QI30_A0A087QI30_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IVJ2_A0A091IVJ2_EGRGA_188379 and tr_A0A093I647_A0A093I647_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091IVJ2_A0A091IVJ2_EGRGA_188379 and tr_A0A099YU04_A0A099YU04_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091IVJ2_A0A091IVJ2_EGRGA_188379 and tr_A0A091FH06_A0A091FH06_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091IVJ2_A0A091IVJ2_EGRGA_188379 and tr_A0A0A0AUH8_A0A0A0AUH8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091IVJ2_A0A091IVJ2_EGRGA_188379 and tr_A0A093IKU1_A0A093IKU1_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091IVJ2_A0A091IVJ2_EGRGA_188379 and tr_A0A091HZS5_A0A091HZS5_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A093HZY9_A0A093HZY9_STRCA_441894 and tr_A0A091IID0_A0A091IID0_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0A0AQ14_A0A0A0AQ14_CHAVO_50402 and tr_A0A093GPZ4_A0A093GPZ4_DRYPU_118200 are exactly identical! WARNING: Duplicate sequences found: 52 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/P56715/4_raxmlng_ancestral/P56715.raxml.reduced.phy Alignment comprises 1 partitions and 2156 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 2156 Gaps: 71.31 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56715/4_raxmlng_ancestral/P56715.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/P56715/3_mltree/P56715.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 539 / 43120 [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: -483595.686286 [00:00:00 -483595.686286] Initial branch length optimization [00:00:06 -376022.483543] Model parameter optimization (eps = 0.100000) [00:02:25] Tree #1, final logLikelihood: -374270.045859 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.060475,0.395317) (0.034096,0.691089) (0.310672,0.638034) (0.594758,1.268266) 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/P56715/4_raxmlng_ancestral/P56715.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56715/4_raxmlng_ancestral/P56715.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56715/4_raxmlng_ancestral/P56715.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56715/4_raxmlng_ancestral/P56715.raxml.log Analysis started: 03-Jun-2021 02:14:14 / finished: 03-Jun-2021 02:16:54 Elapsed time: 159.775 seconds Consumed energy: 8.546 Wh