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 17:56:09 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/2_msa/Q7Z5H3_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/3_mltree/Q7Z5H3.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/4_raxmlng_ancestral/Q7Z5H3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101769 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/Q7Z5H3/2_msa/Q7Z5H3_nogap_msa.fasta [00:00:00] Loaded alignment with 995 taxa and 698 sites WARNING: Sequences tr_A0A2I2ZFN0_A0A2I2ZFN0_GORGO_9595 and tr_A0A2I3SMH6_A0A2I3SMH6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_H2R1I1_H2R1I1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and sp_Q7Z6B7_SRGP1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_G7N7I9_G7N7I9_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_A0A2I3MQK2_A0A2I3MQK2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_A0A0D9QWU6_A0A0D9QWU6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_A0A2K5MYI2_A0A2K5MYI2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_A0A2R9CEY3_A0A2R9CEY3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2N3Y4_H2N3Y4_PONAB_9601 and tr_K7AGG6_K7AGG6_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2N3Y4_H2N3Y4_PONAB_9601 and sp_O75044_SRGP2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2N3Y4_H2N3Y4_PONAB_9601 and tr_A0A2R9C1H1_A0A2R9C1H1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PA60_H2PA60_PONAB_9601 and tr_A0A0D9REF0_A0A0D9REF0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F1PJZ0_F1PJZ0_CANLF_9615 and tr_M3W9I0_M3W9I0_FELCA_9685 are exactly identical! WARNING: Sequences tr_H2QAT1_H2QAT1_PANTR_9598 and sp_Q68EM7_RHG17_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QD90_H2QD90_PANTR_9598 and sp_Q6ZUM4_RHG27_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F1M5M9_F1M5M9_RAT_10116 and tr_A0A1U7Q8L6_A0A1U7Q8L6_MESAU_10036 are exactly identical! WARNING: Sequences tr_F6T0E0_F6T0E0_MACMU_9544 and tr_G7PQA9_G7PQA9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6T0E0_F6T0E0_MACMU_9544 and tr_A0A2K6E3J3_A0A2K6E3J3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B042_F7B042_MACMU_9544 and tr_A0A2I3MCP4_A0A2I3MCP4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7B042_F7B042_MACMU_9544 and tr_A0A2K5LLX3_A0A2K5LLX3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7B042_F7B042_MACMU_9544 and tr_A0A2K6CR26_A0A2K6CR26_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MER6_G7MER6_MACMU_9544 and tr_G7NVB6_G7NVB6_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7MER6_G7MER6_MACMU_9544 and tr_A0A096NE71_A0A096NE71_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7MER6_G7MER6_MACMU_9544 and tr_A0A0D9RQX3_A0A0D9RQX3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7MER6_G7MER6_MACMU_9544 and tr_A0A2K6C966_A0A2K6C966_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MER6_G7MER6_MACMU_9544 and tr_A0A2K6A7C7_A0A2K6A7C7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3SW94_G3SW94_LOXAF_9785 and tr_A0A2Y9D5T9_A0A2Y9D5T9_TRIMA_127582 are exactly identical! WARNING: Sequences tr_U3EWI2_U3EWI2_CALJA_9483 and tr_G7NYV5_G7NYV5_MACFA_9541 are exactly identical! WARNING: Sequences tr_U3EWI2_U3EWI2_CALJA_9483 and tr_A0A096NA88_A0A096NA88_PAPAN_9555 are exactly identical! WARNING: Sequences tr_U3EWI2_U3EWI2_CALJA_9483 and tr_A0A2K5N7D9_A0A2K5N7D9_CERAT_9531 are exactly identical! WARNING: Sequences tr_U3EWI2_U3EWI2_CALJA_9483 and tr_A0A2K6BDV8_A0A2K6BDV8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1MID0_G1MID0_AILME_9646 and tr_A0A384BIU0_A0A384BIU0_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3MMU9_A0A2I3MMU9_PAPAN_9555 and tr_A0A2K5M1L1_A0A2K5M1L1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9R051_A0A0D9R051_CHLSB_60711 and tr_A0A2K5NY60_A0A2K5NY60_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9R051_A0A0D9R051_CHLSB_60711 and tr_A0A2K5YJ75_A0A2K5YJ75_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091JKJ3_A0A091JKJ3_EGRGA_188379 and tr_A0A091UX50_A0A091UX50_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A087R5K3_A0A087R5K3_APTFO_9233 and tr_A0A091GF41_A0A091GF41_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A087R5K3_A0A087R5K3_APTFO_9233 and tr_A0A093GMK4_A0A093GMK4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A0V0WP24_A0A0V0WP24_9BILA_92179 and tr_A0A0V1NU21_A0A0V1NU21_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A2N5SJ60_A0A2N5SJ60_9BASI_200324 and tr_A0A2N5TFF1_A0A2N5TFF1_9BASI_200324 are exactly identical! WARNING: Sequences tr_A0A2U4CQS9_A0A2U4CQS9_TURTR_9739 and tr_A0A2Y9N7F0_A0A2Y9N7F0_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 41 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/Q7Z5H3/4_raxmlng_ancestral/Q7Z5H3.raxml.reduced.phy Alignment comprises 1 partitions and 698 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 698 Gaps: 31.96 % Invariant sites: 0.29 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/4_raxmlng_ancestral/Q7Z5H3.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/Q7Z5H3/3_mltree/Q7Z5H3.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: -262194.227079 [00:00:00 -262194.227079] Initial branch length optimization [00:00:01 -241203.867019] Model parameter optimization (eps = 0.100000) [00:00:57] Tree #1, final logLikelihood: -240737.637138 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.051859,0.187656) (0.078112,0.233868) (0.352122,0.656610) (0.517908,1.430359) 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/Q7Z5H3/4_raxmlng_ancestral/Q7Z5H3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/4_raxmlng_ancestral/Q7Z5H3.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/4_raxmlng_ancestral/Q7Z5H3.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/4_raxmlng_ancestral/Q7Z5H3.raxml.log Analysis started: 12-Jul-2021 17:56:09 / finished: 12-Jul-2021 17:57:13 Elapsed time: 64.133 seconds Consumed energy: 3.914 Wh