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 12-Jul-2021 17:45:25 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/2_msa/Q8TE85_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/3_mltree/Q8TE85.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/4_raxmlng_ancestral/Q8TE85 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101125 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/Q8TE85/2_msa/Q8TE85_nogap_msa.fasta [00:00:00] Loaded alignment with 812 taxa and 626 sites WARNING: Sequences tr_B4QBS0_B4QBS0_DROSI_7240 and tr_B4HN88_B4HN88_DROSE_7238 are exactly identical! WARNING: Sequences tr_A7VJA9_A7VJA9_CHICK_9031 and sp_Q7T2U9_TFCP2_CHICK_9031 are exactly identical! WARNING: Sequences tr_A7VJA9_A7VJA9_CHICK_9031 and tr_A0A226MN10_A0A226MN10_CALSU_9009 are exactly identical! WARNING: Sequences tr_A7VJA9_A7VJA9_CHICK_9031 and tr_A0A226NPV0_A0A226NPV0_COLVI_9014 are exactly identical! WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_H2NHB0_H2NHB0_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_A0A2I3RVQ9_A0A2I3RVQ9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_H0WXF7_H0WXF7_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and sp_Q12800_TFCP2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_F7H1F4_F7H1F4_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_A0A096MPC0_A0A096MPC0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_A0A0D9R0S6_A0A0D9R0S6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_A0A2K5MG93_A0A2K5MG93_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S7V0_G1S7V0_NOMLE_61853 and tr_A0A2R8ZHD7_A0A2R8ZHD7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1PNW8_G1PNW8_MYOLU_59463 and tr_A4FUY6_A4FUY6_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1PNW8_G1PNW8_MYOLU_59463 and tr_A0A2U4CBI7_A0A2U4CBI7_TURTR_9739 are exactly identical! WARNING: Sequences tr_G1PNW8_G1PNW8_MYOLU_59463 and tr_A0A2Y9NF35_A0A2Y9NF35_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1PNW8_G1PNW8_MYOLU_59463 and tr_A0A2Y9F4B4_A0A2Y9F4B4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G3RZF0_G3RZF0_GORGO_9595 and tr_H2QIN0_H2QIN0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RZF0_G3RZF0_GORGO_9595 and sp_Q9NZI6_TF2L1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RZF0_G3RZF0_GORGO_9595 and tr_A0A1D5R5F6_A0A1D5R5F6_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RZF0_G3RZF0_GORGO_9595 and tr_A0A0D9RVU4_A0A0D9RVU4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RZF0_G3RZF0_GORGO_9595 and tr_A0A2K6DJU4_A0A2K6DJU4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3SG69_G3SG69_GORGO_9595 and tr_H2QWI7_H2QWI7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SG69_G3SG69_GORGO_9595 and sp_Q6ISB3_GRHL2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1NGZ9_G1NGZ9_MELGA_9103 and tr_U3I248_U3I248_ANAPL_8839 are exactly identical! WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_F6TYZ0_F6TYZ0_HORSE_9796 are exactly identical! WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_I3MCZ2_I3MCZ2_ICTTR_43179 are exactly identical! WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_M3XA11_M3XA11_FELCA_9685 are exactly identical! WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_A0A091DK05_A0A091DK05_FUKDA_885580 are exactly identical! WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_A0A2U3XUS3_A0A2U3XUS3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_A0A2Y9KQF5_A0A2Y9KQF5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_E2QY24_E2QY24_CANLF_9615 and tr_A0A384D7Q7_A0A384D7Q7_URSMA_29073 are exactly identical! WARNING: Sequences tr_F6SYN6_F6SYN6_MONDO_13616 and tr_G3WLK8_G3WLK8_SARHA_9305 are exactly identical! WARNING: Sequences tr_A0A158Q140_A0A158Q140_BRUMA_6279 and tr_A0A158PSE0_A0A158PSE0_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A015KTX4_A0A015KTX4_9GLOM_1432141 and tr_A0A2H5R4A7_A0A2H5R4A7_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A096MXW7_A0A096MXW7_PAPAN_9555 and tr_A0A0D9RHT7_A0A0D9RHT7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A0A1P0C5_A0A0A1P0C5_9FUNG_58291 and tr_A0A367JBW1_A0A367JBW1_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0Q3MPC7_A0A0Q3MPC7_AMAAE_12930 and tr_A0A1V4K5W1_A0A1V4K5W1_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A091UMX2_A0A091UMX2_NIPNI_128390 and tr_A0A087QTW7_A0A087QTW7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UMX2_A0A091UMX2_NIPNI_128390 and tr_A0A091WHQ3_A0A091WHQ3_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091UMX2_A0A091UMX2_NIPNI_128390 and tr_A0A0A0AML9_A0A0A0AML9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091UMX2_A0A091UMX2_NIPNI_128390 and tr_A0A093FZV6_A0A093FZV6_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091V198_A0A091V198_NIPNI_128390 and tr_A0A087QNZ0_A0A087QNZ0_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091V198_A0A091V198_NIPNI_128390 and tr_A0A091W4H8_A0A091W4H8_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A2I0MWG8_A0A2I0MWG8_COLLI_8932 and tr_A0A1V4KH52_A0A1V4KH52_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CLQ6_A0A0V1CLQ6_TRIBR_45882 and tr_A0A0V0UWJ2_A0A0V0UWJ2_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1P1Z5_A0A0V1P1Z5_9BILA_92180 and tr_A0A0V0U9F4_A0A0V0U9F4_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3MGB0_A0A1S3MGB0_SALSA_8030 and tr_A0A060WEV4_A0A060WEV4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226MS04_A0A226MS04_CALSU_9009 and tr_A0A226PLZ0_A0A226PLZ0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RM34_A0A2D0RM34_ICTPU_7998 and tr_A0A2D0RM37_A0A2D0RM37_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RM34_A0A2D0RM34_ICTPU_7998 and tr_A0A2D0RM42_A0A2D0RM42_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RM34_A0A2D0RM34_ICTPU_7998 and tr_A0A2D0RNP3_A0A2D0RNP3_ICTPU_7998 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/300621_run/phylogeny-snakemake/results/Q8TE85/4_raxmlng_ancestral/Q8TE85.raxml.reduced.phy Alignment comprises 1 partitions and 626 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 626 Gaps: 33.64 % Invariant sites: 0.32 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/4_raxmlng_ancestral/Q8TE85.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/Q8TE85/3_mltree/Q8TE85.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 157 / 12560 [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: -140947.351784 [00:00:00 -140947.351784] Initial branch length optimization [00:00:01 -139477.539473] Model parameter optimization (eps = 0.100000) [00:00:31] Tree #1, final logLikelihood: -139140.043803 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.096318,0.270170) (0.115778,0.332182) (0.306915,0.655294) (0.480989,1.526852) 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/Q8TE85/4_raxmlng_ancestral/Q8TE85.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/4_raxmlng_ancestral/Q8TE85.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/4_raxmlng_ancestral/Q8TE85.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE85/4_raxmlng_ancestral/Q8TE85.raxml.log Analysis started: 12-Jul-2021 17:45:25 / finished: 12-Jul-2021 17:46:01 Elapsed time: 35.574 seconds Consumed energy: 2.379 Wh