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 02-Jun-2021 18:40:08 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZU2/2_msa/Q9GZU2_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZU2/3_mltree/Q9GZU2.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZU2/4_raxmlng_ancestral/Q9GZU2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622648408 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/Q9GZU2/2_msa/Q9GZU2_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1588 sites WARNING: Sequences tr_A0A2I2YQQ8_A0A2I2YQQ8_GORGO_9595 and sp_Q9Y2G7_ZFP30_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZTG0_A0A2I2ZTG0_GORGO_9595 and sp_P17036_ZNF3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TER9_A0A2I3TER9_PANTR_9598 and tr_A0A2R9APU5_A0A2R9APU5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TSX8_A0A2I3TSX8_PANTR_9598 and tr_A0A2R9C1J6_A0A2R9C1J6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8QIH1_A0A2J8QIH1_PANTR_9598 and tr_A0A2R9AKC8_A0A2R9AKC8_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QG63_H2QG63_PANTR_9598 and sp_Q8N141_ZFP82_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7D7J1_K7D7J1_PANTR_9598 and tr_A0A2R9APT9_A0A2R9APT9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5RIP3_A0A1D5RIP3_MACMU_9544 and tr_G8F608_G8F608_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5RIP3_A0A1D5RIP3_MACMU_9544 and tr_A0A2K6CYT4_A0A2K6CYT4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A2K5MYE8_A0A2K5MYE8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A2K5ZQH5_A0A2K5ZQH5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6X482_F6X482_MACMU_9544 and tr_G7PER6_G7PER6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6X482_F6X482_MACMU_9544 and tr_A0A2K6C6G6_A0A2K6C6G6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DJ47_F7DJ47_MACMU_9544 and tr_A0A2K5LZU4_A0A2K5LZU4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DJ47_F7DJ47_MACMU_9544 and tr_A0A2K6BPR5_A0A2K6BPR5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7F0N9_F7F0N9_MACMU_9544 and tr_A0A2K5LZF8_A0A2K5LZF8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7F0N9_F7F0N9_MACMU_9544 and tr_A0A2K6B2T5_A0A2K6B2T5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7F0N9_F7F0N9_MACMU_9544 and tr_A0A2K5YGT5_A0A2K5YGT5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7FX09_F7FX09_MACMU_9544 and tr_A0A2K6B732_A0A2K6B732_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HT77_F7HT77_MACMU_9544 and tr_A0A096P104_A0A096P104_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7MUI1_G7MUI1_MACMU_9544 and tr_A0A2K6AN26_A0A2K6AN26_MACNE_9545 are exactly identical! WARNING: Sequences tr_H9ERQ6_H9ERQ6_MACMU_9544 and tr_A0A2K6D8Q9_A0A2K6D8Q9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1L1C1_G1L1C1_AILME_9646 and tr_A0A384DGZ4_A0A384DGZ4_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7P0C3_G7P0C3_MACFA_9541 and tr_A0A0D9RZ15_A0A0D9RZ15_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7P0C3_G7P0C3_MACFA_9541 and tr_A0A2K6DHH7_A0A2K6DHH7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PRT6_G7PRT6_MACFA_9541 and tr_A0A2K5KKJ7_A0A2K5KKJ7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PRT6_G7PRT6_MACFA_9541 and tr_A0A2K6E2Z0_A0A2K6E2Z0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PRT6_G7PRT6_MACFA_9541 and tr_A0A2K5YQK9_A0A2K5YQK9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7PXD8_G7PXD8_MACFA_9541 and tr_A0A0D9SB33_A0A0D9SB33_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7Q1K4_G7Q1K4_MACFA_9541 and tr_A0A2K6CVH8_A0A2K6CVH8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F1MBU3_F1MBU3_BOVIN_9913 and sp_Q6H236_PEG3_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A096MQ78_A0A096MQ78_PAPAN_9555 and tr_A0A2K5ZGD5_A0A2K5ZGD5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096MQW2_A0A096MQW2_PAPAN_9555 and tr_A0A2K5KVJ5_A0A2K5KVJ5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MQW2_A0A096MQW2_PAPAN_9555 and tr_A0A2K5XIU1_A0A2K5XIU1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096P472_A0A096P472_PAPAN_9555 and tr_A0A2K5ZDY2_A0A2K5ZDY2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0MUX4_A0A0A0MUX4_PAPAN_9555 and tr_A0A2K5KRM5_A0A2K5KRM5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MEB8_A0A2I3MEB8_PAPAN_9555 and tr_A0A2K5NZC2_A0A2K5NZC2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2U4AZ32_A0A2U4AZ32_TURTR_9739 and tr_A0A2Y9PC28_A0A2Y9PC28_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CGU5_A0A2U4CGU5_TURTR_9739 and tr_A0A2Y9QA60_A0A2Y9QA60_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 39 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/Q9GZU2/4_raxmlng_ancestral/Q9GZU2.raxml.reduced.phy Alignment comprises 1 partitions and 1588 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1588 Gaps: 67.20 % Invariant sites: 2.52 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZU2/4_raxmlng_ancestral/Q9GZU2.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/Q9GZU2/3_mltree/Q9GZU2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 397 / 31760 [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: -265727.749874 [00:00:00 -265727.749874] Initial branch length optimization [00:00:03 -263822.066518] Model parameter optimization (eps = 0.100000) [00:01:43] Tree #1, final logLikelihood: -263200.525400 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.072299,0.152000) (0.084283,0.444019) (0.347784,0.637483) (0.495635,1.472619) 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/Q9GZU2/4_raxmlng_ancestral/Q9GZU2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZU2/4_raxmlng_ancestral/Q9GZU2.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZU2/4_raxmlng_ancestral/Q9GZU2.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZU2/4_raxmlng_ancestral/Q9GZU2.raxml.log Analysis started: 02-Jun-2021 18:40:08 / finished: 02-Jun-2021 18:42:07 Elapsed time: 118.957 seconds Consumed energy: 7.526 Wh