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 02-Jun-2021 15:03:03 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9HB58/2_msa/Q9HB58_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9HB58/3_mltree/Q9HB58.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9HB58/4_raxmlng_ancestral/Q9HB58 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622635383 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/Q9HB58/2_msa/Q9HB58_nogap_msa.fasta [00:00:00] Loaded alignment with 828 taxa and 689 sites WARNING: Sequences tr_A0A2R8RZL6_A0A2R8RZL6_DANRE_7955 and tr_X1WDS1_X1WDS1_DANRE_7955 are exactly identical! WARNING: Sequences tr_G1QSG2_G1QSG2_NOMLE_61853 and tr_H2NT56_H2NT56_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1PMZ7_G1PMZ7_MYOLU_59463 and tr_G1T8Z6_G1T8Z6_RABIT_9986 are exactly identical! WARNING: Sequences tr_G1PMZ7_G1PMZ7_MYOLU_59463 and tr_E2QYC0_E2QYC0_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1PMZ7_G1PMZ7_MYOLU_59463 and tr_F6YH99_F6YH99_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1PMZ7_G1PMZ7_MYOLU_59463 and tr_A0A1D5RA83_A0A1D5RA83_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1PMZ7_G1PMZ7_MYOLU_59463 and tr_G3TC47_G3TC47_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G1PMZ7_G1PMZ7_MYOLU_59463 and tr_L5JSX8_L5JSX8_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1PMZ7_G1PMZ7_MYOLU_59463 and tr_M3W6Z4_M3W6Z4_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1PMZ7_G1PMZ7_MYOLU_59463 and tr_A0A096P3F6_A0A096P3F6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1PMZ7_G1PMZ7_MYOLU_59463 and tr_A0A0D9R412_A0A0D9R412_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1PMZ7_G1PMZ7_MYOLU_59463 and tr_A0A2K5LMP1_A0A2K5LMP1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1PMZ7_G1PMZ7_MYOLU_59463 and tr_A0A2K6CE12_A0A2K6CE12_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1PMZ7_G1PMZ7_MYOLU_59463 and tr_A0A2Y9JUZ0_A0A2Y9JUZ0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_B7XK84_B7XK84_ENTBH_481877 and tr_B7XKW6_B7XKW6_ENTBH_481877 are exactly identical! WARNING: Sequences tr_B7XK84_B7XK84_ENTBH_481877 and tr_B7XM17_B7XM17_ENTBH_481877 are exactly identical! WARNING: Sequences tr_B7XK84_B7XK84_ENTBH_481877 and tr_B7XNR8_B7XNR8_ENTBH_481877 are exactly identical! WARNING: Sequences tr_B7XK84_B7XK84_ENTBH_481877 and tr_B7XPA6_B7XPA6_ENTBH_481877 are exactly identical! WARNING: Sequences tr_A0A2I3SB75_A0A2I3SB75_PANTR_9598 and sp_Q8TDI0_CHD5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TUL5_A0A2I3TUL5_PANTR_9598 and tr_A0A2R9B596_A0A2R9B596_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCJ8_H2QCJ8_PANTR_9598 and sp_Q96QT6_PHF12_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QCJ8_H2QCJ8_PANTR_9598 and tr_A0A2R9CQS1_A0A2R9CQS1_PANPA_9597 are exactly identical! WARNING: Sequences sp_O15164_TIF1A_HUMAN_9606 and tr_F6VVE4_F6VVE4_MACMU_9544 are exactly identical! WARNING: Sequences sp_O15164_TIF1A_HUMAN_9606 and tr_A0A2K5LKM0_A0A2K5LKM0_CERAT_9531 are exactly identical! WARNING: Sequences sp_O15164_TIF1A_HUMAN_9606 and tr_A0A2K6DBD8_A0A2K6DBD8_MACNE_9545 are exactly identical! WARNING: Sequences sp_O15164_TIF1A_HUMAN_9606 and tr_A0A2R8ZN70_A0A2R8ZN70_PANPA_9597 are exactly identical! WARNING: Sequences tr_G5BVJ1_G5BVJ1_HETGA_10181 and tr_A0A091D4X7_A0A091D4X7_FUKDA_885580 are exactly identical! WARNING: Sequences tr_B8B6D8_B8B6D8_ORYSI_39946 and tr_A0A0E0Q8L0_A0A0E0Q8L0_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1QAU8_I1QAU8_ORYGL_4538 and tr_I1QWL9_I1QWL9_ORYGL_4538 are exactly identical! WARNING: Sequences tr_I1QAU8_I1QAU8_ORYGL_4538 and tr_A0A0E0AK64_A0A0E0AK64_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_U3JV06_U3JV06_FICAL_59894 and tr_A0A1V4K2J6_A0A1V4K2J6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A015L1T0_A0A015L1T0_9GLOM_1432141 and tr_A0A2H5U225_A0A2H5U225_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044V850_A0A044V850_ONCVO_6282 and tr_A0A182E7I9_A0A182E7I9_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A1S3ZWA3_A0A1S3ZWA3_TOBAC_4097 and tr_A0A1U7YX65_A0A1U7YX65_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3JUG8_A0A1S3JUG8_LINUN_7574 and tr_A0A1S3JVC9_A0A1S3JVC9_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A2D0SK97_A0A2D0SK97_ICTPU_7998 and tr_A0A2D0SLG7_A0A2D0SLG7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4CGU1_A0A2U4CGU1_TURTR_9739 and tr_A0A2Y9NPI3_A0A2Y9NPI3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CGU1_A0A2U4CGU1_TURTR_9739 and tr_A0A2Y9TA18_A0A2Y9TA18_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9Q8S7_A0A2Y9Q8S7_DELLE_9749 and tr_A0A2Y9FFQ3_A0A2Y9FFQ3_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9Q8S7_A0A2Y9Q8S7_DELLE_9749 and tr_A0A384A9I8_A0A384A9I8_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 40 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/Q9HB58/4_raxmlng_ancestral/Q9HB58.raxml.reduced.phy Alignment comprises 1 partitions and 689 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 689 Gaps: 58.05 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9HB58/4_raxmlng_ancestral/Q9HB58.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/Q9HB58/3_mltree/Q9HB58.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 173 / 13840 [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: -330807.306184 [00:00:00 -330807.306184] Initial branch length optimization [00:00:02 -236207.155491] Model parameter optimization (eps = 0.100000) [00:01:06] Tree #1, final logLikelihood: -235186.733969 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.113867,0.590616) (0.043840,0.942136) (0.293906,0.724025) (0.548386,1.237538) 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/Q9HB58/4_raxmlng_ancestral/Q9HB58.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9HB58/4_raxmlng_ancestral/Q9HB58.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9HB58/4_raxmlng_ancestral/Q9HB58.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9HB58/4_raxmlng_ancestral/Q9HB58.raxml.log Analysis started: 02-Jun-2021 15:03:03 / finished: 02-Jun-2021 15:04:15 Elapsed time: 71.229 seconds