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 02:37:40 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19429/2_msa/P19429_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19429/3_mltree/P19429.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19429/4_raxmlng_ancestral/P19429 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677060 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/P19429/2_msa/P19429_nogap_msa.fasta [00:00:00] Loaded alignment with 553 taxa and 210 sites WARNING: Sequences sp_Q9WUZ5_TNNI1_MOUSE_10090 and sp_P13413_TNNI1_RAT_10116 are exactly identical! WARNING: Sequences sp_P36188_TNNI_DROME_7227 and tr_B4JKX9_B4JKX9_DROGR_7222 are exactly identical! WARNING: Sequences sp_P36188_TNNI_DROME_7227 and tr_A0A0M4EYL5_A0A0M4EYL5_DROBS_30019 are exactly identical! WARNING: Sequences sp_P36188_TNNI_DROME_7227 and tr_A0A1W4V252_A0A1W4V252_DROFC_30025 are exactly identical! WARNING: Sequences tr_A0A2I3G862_A0A2I3G862_NOMLE_61853 and tr_G3RAC1_G3RAC1_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3G862_A0A2I3G862_NOMLE_61853 and tr_H2Q0V9_H2Q0V9_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3G862_A0A2I3G862_NOMLE_61853 and sp_P19237_TNNI1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3G862_A0A2I3G862_NOMLE_61853 and tr_A0A2I3LJQ7_A0A2I3LJQ7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2J8S6R9_A0A2J8S6R9_PONAB_9601 and sp_P48788_TNNI2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2P0U7_H2P0U7_PONAB_9601 and tr_G7NWF5_G7NWF5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F1PLD6_F1PLD6_CANLF_9615 and tr_A0A2I2UV91_A0A2I2UV91_FELCA_9685 are exactly identical! WARNING: Sequences sp_P19429_TNNI3_HUMAN_9606 and tr_A0A2R9ATT7_A0A2R9ATT7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QBP4_A0A1D5QBP4_MACMU_9544 and tr_A0A2R8ZRU1_A0A2R8ZRU1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A8XQV8_A8XQV8_CAEBR_6238 and tr_A0A2G5SNY2_A0A2G5SNY2_9PELO_1611254 are exactly identical! WARNING: Sequences tr_A0A3Q0KCV6_A0A3Q0KCV6_SCHMA_6183 and tr_G4VGQ7_G4VGQ7_SCHMA_6183 are exactly identical! WARNING: Sequences tr_A0A3Q0KGG6_A0A3Q0KGG6_SCHMA_6183 and tr_G4VJ45_G4VJ45_SCHMA_6183 are exactly identical! WARNING: Sequences tr_A0A044TX11_A0A044TX11_ONCVO_6282 and tr_A0A182E5Z2_A0A182E5Z2_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A2I3LP77_A0A2I3LP77_PAPAN_9555 and tr_A0A2K5KZ54_A0A2K5KZ54_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9S5X9_A0A0D9S5X9_CHLSB_60711 and tr_A0A2K5MIT2_A0A2K5MIT2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9S5X9_A0A0D9S5X9_CHLSB_60711 and tr_A0A2K6CRE7_A0A2K6CRE7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D9S5X9_A0A0D9S5X9_CHLSB_60711 and tr_A0A2K5Z5W7_A0A2K5Z5W7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0K0FF53_A0A0K0FF53_STRVS_75913 and tr_A0A0N5B387_A0A0N5B387_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0N4T6P0_A0A0N4T6P0_BRUPA_6280 and tr_A0A0R3QMH6_A0A0R3QMH6_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A093QHE6_A0A093QHE6_9PASS_328815 and tr_A0A0A0A8N3_A0A0A0A8N3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091VMS5_A0A091VMS5_NIPNI_128390 and tr_A0A087RK33_A0A087RK33_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A0V0S151_A0A0V0S151_9BILA_6336 and tr_A0A0V1CEQ8_A0A0V1CEQ8_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0S151_A0A0V0S151_9BILA_6336 and tr_A0A0V0W7Z0_A0A0V0W7Z0_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0S151_A0A0V0S151_9BILA_6336 and tr_A0A0V0UV72_A0A0V0UV72_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0S151_A0A0V0S151_9BILA_6336 and tr_A0A0V1LDI3_A0A0V1LDI3_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0S151_A0A0V0S151_9BILA_6336 and tr_A0A0V0ZAL5_A0A0V0ZAL5_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0S151_A0A0V0S151_9BILA_6336 and tr_A0A0V0XL13_A0A0V0XL13_TRIPS_6337 are exactly identical! WARNING: Sequences tr_A0A0V0S151_A0A0V0S151_9BILA_6336 and tr_A0A0V1P5M6_A0A0V1P5M6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0S151_A0A0V0S151_9BILA_6336 and tr_A0A0V1GVM0_A0A0V1GVM0_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A0V0S151_A0A0V0S151_9BILA_6336 and tr_A0A0V0TDJ3_A0A0V0TDJ3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1I7TR51_A0A1I7TR51_9PELO_1561998 and tr_A0A1I7TR52_A0A1I7TR52_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A2K5KZH1_A0A2K5KZH1_CERAT_9531 and tr_A0A2K6DMG3_A0A2K6DMG3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5KZH1_A0A2K5KZH1_CERAT_9531 and tr_A0A2K5Y629_A0A2K5Y629_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K6B510_A0A2K6B510_MACNE_9545 and tr_A0A2K5Z8A9_A0A2K5Z8A9_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 38 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/P19429/4_raxmlng_ancestral/P19429.raxml.reduced.phy Alignment comprises 1 partitions and 210 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 210 Gaps: 19.72 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19429/4_raxmlng_ancestral/P19429.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/P19429/3_mltree/P19429.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 53 / 4240 [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: -40692.447926 [00:00:00 -40692.447926] Initial branch length optimization [00:00:00 -40382.084854] Model parameter optimization (eps = 0.100000) [00:00:14] Tree #1, final logLikelihood: -40288.335225 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.116690,0.219656) (0.087568,0.309269) (0.406683,0.647362) (0.389058,1.758130) 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/P19429/4_raxmlng_ancestral/P19429.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19429/4_raxmlng_ancestral/P19429.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19429/4_raxmlng_ancestral/P19429.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P19429/4_raxmlng_ancestral/P19429.raxml.log Analysis started: 03-Jun-2021 02:37:40 / finished: 03-Jun-2021 02:37:56 Elapsed time: 15.997 seconds Consumed energy: 1.179 Wh