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 12-Jul-2021 17:57:36 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2KJY2/2_msa/Q2KJY2_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2KJY2/3_mltree/Q2KJY2.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2KJY2/4_raxmlng_ancestral/Q2KJY2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101856 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/300621_run/phylogeny-snakemake/results/Q2KJY2/2_msa/Q2KJY2_nogap_msa.fasta [00:00:00] Loaded alignment with 987 taxa and 2108 sites WARNING: Sequences tr_Q5F423_Q5F423_CHICK_9031 and tr_G1N6G9_G1N6G9_MELGA_9103 are exactly identical! WARNING: Sequences tr_M3Z2F0_M3Z2F0_MUSPF_9669 and tr_E2QUS2_E2QUS2_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z2F0_M3Z2F0_MUSPF_9669 and tr_G1M429_G1M429_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z2F0_M3Z2F0_MUSPF_9669 and tr_M3X169_M3X169_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2I3HFJ1_A0A2I3HFJ1_NOMLE_61853 and tr_G7P888_G7P888_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QY97_G3QY97_GORGO_9595 and tr_A0A2I3RF17_A0A2I3RF17_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QY97_G3QY97_GORGO_9595 and sp_Q9Y496_KIF3A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QY97_G3QY97_GORGO_9595 and tr_A0A2R9BCA2_A0A2R9BCA2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QK62_H2QK62_PANTR_9598 and sp_O15066_KIF3B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QK62_H2QK62_PANTR_9598 and tr_A0A096NUY3_A0A096NUY3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2QK62_H2QK62_PANTR_9598 and tr_A0A2K5L083_A0A2K5L083_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2QK62_H2QK62_PANTR_9598 and tr_A0A2R9BB24_A0A2R9BB24_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5NZV7_W5NZV7_SHEEP_9940 and tr_F1N020_F1N020_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A158NZT6_A0A158NZT6_ATTCE_12957 and tr_A0A195BMG4_A0A195BMG4_9HYME_520822 are exactly identical! WARNING: Sequences tr_F6S877_F6S877_MACMU_9544 and tr_G7PGM8_G7PGM8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6S877_F6S877_MACMU_9544 and tr_A0A2K6D218_A0A2K6D218_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BR30_F7BR30_MACMU_9544 and tr_F7EXN8_F7EXN8_CALJA_9483 are exactly identical! WARNING: Sequences tr_F7BR30_F7BR30_MACMU_9544 and tr_A0A2K6BIR9_A0A2K6BIR9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7XM93_G7XM93_ASPKW_1033177 and tr_A0A100IPV7_A0A100IPV7_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XM93_G7XM93_ASPKW_1033177 and tr_A0A146FAM8_A0A146FAM8_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XM93_G7XM93_ASPKW_1033177 and tr_A0A1L9NQF7_A0A1L9NQF7_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G7XM93_G7XM93_ASPKW_1033177 and tr_A0A317UWU6_A0A317UWU6_9EURO_1448314 are exactly identical! WARNING: Sequences tr_G3T0G8_G3T0G8_LOXAF_9785 and tr_A0A2Y9QI24_A0A2Y9QI24_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A0A2I2U4Q8_A0A2I2U4Q8_FELCA_9685 and tr_A0A2U3WHS7_A0A2U3WHS7_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I2U4Q8_A0A2I2U4Q8_FELCA_9685 and tr_A0A2U3XTG2_A0A2U3XTG2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_W2PPA8_W2PPA8_PHYPN_761204 and tr_A0A0W8D6C7_A0A0W8D6C7_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PPA8_W2PPA8_PHYPN_761204 and tr_W2KCI8_W2KCI8_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2PZR3_W2PZR3_PHYPN_761204 and tr_W2KWP2_W2KWP2_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2Q0C1_W2Q0C1_PHYPN_761204 and tr_A0A0W8DVX0_A0A0W8DVX0_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A091J8C0_A0A091J8C0_EGRGA_188379 and tr_A0A091WS06_A0A091WS06_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091J8C0_A0A091J8C0_EGRGA_188379 and tr_A0A087R2P0_A0A087R2P0_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091J8C0_A0A091J8C0_EGRGA_188379 and tr_A0A0A0B3W6_A0A0A0B3W6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087RF52_A0A087RF52_APTFO_9233 and tr_A0A0A0A1U0_A0A0A0A1U0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1CHN2_A0A0V1CHN2_TRIBR_45882 and tr_A0A0V1KUC4_A0A0V1KUC4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CHN2_A0A0V1CHN2_TRIBR_45882 and tr_A0A0V1P260_A0A0V1P260_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CHN2_A0A0V1CHN2_TRIBR_45882 and tr_A0A0V0TJ09_A0A0V0TJ09_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A226MF24_A0A226MF24_CALSU_9009 and tr_A0A226PF49_A0A226PF49_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MHI2_A0A226MHI2_CALSU_9009 and tr_A0A226P9V5_A0A226P9V5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NJV1_A0A226NJV1_CALSU_9009 and tr_A0A226PII5_A0A226PII5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PKW6_A0A2D0PKW6_ICTPU_7998 and tr_A0A2D0PMJ4_A0A2D0PMJ4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PKW6_A0A2D0PKW6_ICTPU_7998 and tr_A0A2D0PNK2_A0A2D0PNK2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2Y9FGM5_A0A2Y9FGM5_PHYCD_9755 and tr_A0A384B241_A0A384B241_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 42 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2KJY2/4_raxmlng_ancestral/Q2KJY2.raxml.reduced.phy Alignment comprises 1 partitions and 2108 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 2108 Gaps: 59.28 % Invariant sites: 0.05 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2KJY2/4_raxmlng_ancestral/Q2KJY2.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/300621_run/phylogeny-snakemake/results/Q2KJY2/3_mltree/Q2KJY2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 527 / 42160 [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: -524950.673800 [00:00:00 -524950.673800] Initial branch length optimization [00:00:05 -497483.302966] Model parameter optimization (eps = 0.100000) [00:02:28] Tree #1, final logLikelihood: -496052.099466 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.067992,0.194622) (0.057037,0.233731) (0.346119,0.639122) (0.528851,1.422373) 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/300621_run/phylogeny-snakemake/results/Q2KJY2/4_raxmlng_ancestral/Q2KJY2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2KJY2/4_raxmlng_ancestral/Q2KJY2.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2KJY2/4_raxmlng_ancestral/Q2KJY2.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2KJY2/4_raxmlng_ancestral/Q2KJY2.raxml.log Analysis started: 12-Jul-2021 17:57:36 / finished: 12-Jul-2021 18:00:25 Elapsed time: 169.436 seconds Consumed energy: 10.640 Wh