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 17:25:23 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q05193/2_msa/Q05193_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q05193/3_mltree/Q05193.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q05193/4_raxmlng_ancestral/Q05193 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099923 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/Q05193/2_msa/Q05193_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 864 sites WARNING: Sequences tr_J3KL22_J3KL22_COCIM_246410 and tr_E9CU59_E9CU59_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3KL22_J3KL22_COCIM_246410 and tr_A0A0J7BHQ3_A0A0J7BHQ3_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QMJ5_B6QMJ5_TALMQ_441960 and tr_A0A093UYG3_A0A093UYG3_TALMA_1077442 are exactly identical! WARNING: Sequences tr_A0A2I2Y8E6_A0A2I2Y8E6_GORGO_9595 and sp_P50570_DYN2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_C0NKN2_C0NKN2_AJECG_447093 and tr_C6HAX1_C6HAX1_AJECH_544712 are exactly identical! WARNING: Sequences tr_C0NKN2_C0NKN2_AJECG_447093 and tr_F0UD31_F0UD31_AJEC8_544711 are exactly identical! WARNING: Sequences tr_Q7SDJ3_Q7SDJ3_NEUCR_367110 and tr_G4U8X4_G4U8X4_NEUT9_510952 are exactly identical! WARNING: Sequences tr_F9F1G4_F9F1G4_FUSOF_660025 and tr_A0A0D2X858_A0A0D2X858_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9F1G4_F9F1G4_FUSOF_660025 and tr_N4U7Q5_N4U7Q5_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9F1G4_F9F1G4_FUSOF_660025 and tr_A0A2H3SV71_A0A2H3SV71_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9F1G4_F9F1G4_FUSOF_660025 and tr_A0A2H3HSI1_A0A2H3HSI1_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9F1G4_F9F1G4_FUSOF_660025 and tr_A0A2K0WDB2_A0A2K0WDB2_GIBNY_42673 are exactly identical! WARNING: Sequences tr_J4UJE8_J4UJE8_BEAB2_655819 and tr_A0A2N6NGU0_A0A2N6NGU0_BEABA_176275 are exactly identical! WARNING: Sequences tr_Q2TVY0_Q2TVY0_ASPOR_510516 and tr_A0A1S9DFU0_A0A1S9DFU0_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A2QHI2_A2QHI2_ASPNC_425011 and tr_G3Y7Y3_G3Y7Y3_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QHI2_A2QHI2_ASPNC_425011 and tr_A0A318ZVQ4_A0A318ZVQ4_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XV65_G7XV65_ASPKW_1033177 and tr_A0A146FYX7_A0A146FYX7_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XV65_G7XV65_ASPKW_1033177 and tr_A0A317V7Y1_A0A317V7Y1_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A0E0CCA3_A0A0E0CCA3_9ORYZ_40149 and tr_Q5JJJ5_Q5JJJ5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F9X1G0_F9X1G0_ZYMTI_336722 and tr_A0A1X7RI49_A0A1X7RI49_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_E3MCH2_E3MCH2_CAERE_31234 and tr_A0A261CPD2_A0A261CPD2_9PELO_1503980 are exactly identical! WARNING: Sequences tr_F2PGK6_F2PGK6_TRIEC_559882 and tr_A0A059J694_A0A059J694_9EURO_1215338 are exactly identical! WARNING: Sequences tr_U5H5W1_U5H5W1_USTV1_683840 and tr_A0A2X0MRI4_A0A2X0MRI4_9BASI_796604 are exactly identical! WARNING: Sequences tr_V2WXT5_V2WXT5_MONRO_1381753 and tr_A0A0W0G2V7_A0A0W0G2V7_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2PU56_W2PU56_PHYPN_761204 and tr_W2KMW5_W2KMW5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A2I3LFI4_A0A2I3LFI4_PAPAN_9555 and tr_A0A2K5N2A2_A0A2K5N2A2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A094E6M2_A0A094E6M2_9PEZI_1420912 and tr_A0A1B8G8K7_A0A1B8G8K7_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0D9RGW8_A0A0D9RGW8_CHLSB_60711 and tr_A0A2K5N1J4_A0A2K5N1J4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9RGW8_A0A0D9RGW8_CHLSB_60711 and tr_A0A2K6E0W7_A0A2K6E0W7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0F8UTH1_A0A0F8UTH1_9EURO_308745 and tr_A0A2T5M5D8_A0A2T5M5D8_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0V0WU03_A0A0V0WU03_9BILA_92179 and tr_A0A0V0UU06_A0A0V0UU06_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0WU03_A0A0V0WU03_9BILA_92179 and tr_A0A0V0TRP0_A0A0V0TRP0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A101MIE0_A0A101MIE0_9EURO_48697 and tr_A0A1V6NE80_A0A1V6NE80_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A101MIE0_A0A101MIE0_9EURO_48697 and tr_A0A1V6R4N0_A0A1V6R4N0_9EURO_60172 are exactly identical! WARNING: Sequences tr_I1RCK2_I1RCK2_GIBZE_229533 and tr_A0A2T4H7N2_A0A2T4H7N2_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A2D0QAZ5_A0A2D0QAZ5_ICTPU_7998 and tr_A0A2D0QC35_A0A2D0QC35_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QC32_A0A2D0QC32_ICTPU_7998 and tr_A0A2D0QER6_A0A2D0QER6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QC42_A0A2D0QC42_ICTPU_7998 and tr_A0A2D0QDR3_A0A2D0QDR3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RDS9_A0A2D0RDS9_ICTPU_7998 and tr_A0A2D0RFM2_A0A2D0RFM2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3VDA2_A0A2U3VDA2_ODORO_9708 and tr_A0A2Y9J6B9_A0A2Y9J6B9_ENHLU_391180 are exactly identical! WARNING: Duplicate sequences found: 40 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/Q05193/4_raxmlng_ancestral/Q05193.raxml.reduced.phy Alignment comprises 1 partitions and 864 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 864 Gaps: 18.52 % Invariant sites: 1.16 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q05193/4_raxmlng_ancestral/Q05193.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/Q05193/3_mltree/Q05193.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 216 / 17280 [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: -235472.799773 [00:00:00 -235472.799773] Initial branch length optimization [00:00:02 -216557.463947] Model parameter optimization (eps = 0.100000) [00:00:47] Tree #1, final logLikelihood: -215962.018988 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.233893,0.237904) (0.207627,0.319843) (0.275691,0.846897) (0.282790,2.278960) 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/Q05193/4_raxmlng_ancestral/Q05193.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q05193/4_raxmlng_ancestral/Q05193.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q05193/4_raxmlng_ancestral/Q05193.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q05193/4_raxmlng_ancestral/Q05193.raxml.log Analysis started: 12-Jul-2021 17:25:23 / finished: 12-Jul-2021 17:26:19 Elapsed time: 56.064 seconds Consumed energy: 4.529 Wh