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 23-Jun-2021 00:36:59 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBK8/2_msa/Q9UBK8_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBK8/3_mltree/Q9UBK8.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBK8/4_raxmlng_ancestral/Q9UBK8 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624397819 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/030621_run/phylogeny-snakemake/results/Q9UBK8/2_msa/Q9UBK8_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 698 sites WARNING: Sequences tr_J3KGJ4_J3KGJ4_COCIM_246410 and tr_A0A0J6XV84_A0A0J6XV84_COCIT_404692 are exactly identical! WARNING: Sequences tr_Q29JN6_Q29JN6_DROPS_46245 and tr_B4GJE2_B4GJE2_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8N8Y9_B8N8Y9_ASPFN_332952 and sp_Q2UHA7_NCPR_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N8Y9_B8N8Y9_ASPFN_332952 and tr_A0A1S9DYG1_A0A1S9DYG1_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UWE8_A0A179UWE8_BLAGS_559298 and tr_C5GMR1_C5GMR1_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2QUS7_H2QUS7_PANTR_9598 and tr_A0A2R9BIH0_A0A2R9BIH0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NEE4_A0A158NEE4_ATTCE_12957 and tr_A0A195BVA0_A0A195BVA0_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0E0I928_A0A0E0I928_ORYNI_4536 and tr_I1QGU2_I1QGU2_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0I928_A0A0E0I928_ORYNI_4536 and tr_A0A0E0ASS8_A0A0E0ASS8_9ORYZ_40148 are exactly identical! WARNING: Sequences sp_A2QS05_NCPR_ASPNC_425011 and tr_G3YEV8_G3YEV8_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A0A1D5Q4C0_A0A1D5Q4C0_MACMU_9544 and tr_A0A0D9RZX8_A0A0D9RZX8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5Q4C0_A0A1D5Q4C0_MACMU_9544 and tr_A0A2K5NDR5_A0A2K5NDR5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5Q4C0_A0A1D5Q4C0_MACMU_9544 and tr_A0A2K6CT48_A0A2K6CT48_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7X732_G7X732_ASPKW_1033177 and tr_A0A146FUW6_A0A146FUW6_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A0A0E0PF07_A0A0E0PF07_ORYRU_4529 and tr_Q7X7K8_Q7X7K8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A5D9D3_A5D9D3_BOVIN_9913 and sp_Q3SYT8_NCPR_BOVIN_9913 are exactly identical! WARNING: Sequences tr_L0P9R8_L0P9R8_PNEJ8_1209962 and tr_A0A0W4ZVW6_A0A0W4ZVW6_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_M4BLU5_M4BLU5_HYAAE_559515 and tr_M4BLU6_M4BLU6_HYAAE_559515 are exactly identical! WARNING: Sequences tr_A0A015JSJ9_A0A015JSJ9_9GLOM_1432141 and tr_U9TFR0_U9TFR0_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A094DVE3_A0A094DVE3_9PEZI_1420912 and tr_A0A1B8GWV6_A0A1B8GWV6_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F8V0B3_A0A0F8V0B3_9EURO_308745 and tr_A0A2T5M3T0_A0A2T5M3T0_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0V1CEA0_A0A0V1CEA0_TRIBR_45882 and tr_A0A0V0V0H1_A0A0V0V0H1_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CEA0_A0A0V1CEA0_TRIBR_45882 and tr_A0A0V1LC41_A0A0V1LC41_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CEA0_A0A0V1CEA0_TRIBR_45882 and tr_A0A0V1NUB7_A0A0V1NUB7_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DFY6_A0A0V1DFY6_TRIBR_45882 and tr_A0A0V0VEZ5_A0A0V0VEZ5_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DFY6_A0A0V1DFY6_TRIBR_45882 and tr_A0A0V1LQI5_A0A0V1LQI5_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DFY6_A0A0V1DFY6_TRIBR_45882 and tr_A0A0V0UE04_A0A0V0UE04_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A117E027_A0A117E027_ASPNG_5061 and tr_A0A1L9NPG0_A0A1L9NPG0_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A1S3X9I1_A0A1S3X9I1_TOBAC_4097 and tr_A0A1U7Y8L3_A0A1U7Y8L3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3K793_A0A1S3K793_LINUN_7574 and tr_A0A1S3K7M5_A0A1S3K7M5_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1U7SMN6_A0A1U7SMN6_ALLSI_38654 and tr_A0A3Q0HJY8_A0A3Q0HJY8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A2Y9PKD2_A0A2Y9PKD2_DELLE_9749 and tr_A0A2Y9PM06_A0A2Y9PM06_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 32 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBK8/4_raxmlng_ancestral/Q9UBK8.raxml.reduced.phy Alignment comprises 1 partitions and 698 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 698 Gaps: 20.67 % Invariant sites: 0.43 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBK8/4_raxmlng_ancestral/Q9UBK8.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/030621_run/phylogeny-snakemake/results/Q9UBK8/3_mltree/Q9UBK8.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 175 / 14000 [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: -320679.073590 [00:00:00 -320679.073590] Initial branch length optimization [00:00:02 -318584.047864] Model parameter optimization (eps = 0.100000) [00:00:45] Tree #1, final logLikelihood: -318036.901618 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.120931,0.222871) (0.210845,0.406703) (0.292524,0.834114) (0.375700,1.712265) 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/030621_run/phylogeny-snakemake/results/Q9UBK8/4_raxmlng_ancestral/Q9UBK8.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBK8/4_raxmlng_ancestral/Q9UBK8.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBK8/4_raxmlng_ancestral/Q9UBK8.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q9UBK8/4_raxmlng_ancestral/Q9UBK8.raxml.log Analysis started: 23-Jun-2021 00:36:59 / finished: 23-Jun-2021 00:37:52 Elapsed time: 52.709 seconds Consumed energy: 4.235 Wh