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 17:25:38 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NK58/2_msa/A6NK58_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NK58/3_mltree/A6NK58.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NK58/4_raxmlng_ancestral/A6NK58 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099938 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/A6NK58/2_msa/A6NK58_nogap_msa.fasta [00:00:00] Loaded alignment with 953 taxa and 231 sites WARNING: Sequences tr_B2WA79_B2WA79_PYRTR_426418 and tr_A0A2W1DVQ3_A0A2W1DVQ3_9PLEO_45151 are exactly identical! WARNING: Sequences tr_D8R3Q9_D8R3Q9_SELML_88036 and tr_D8SIE8_D8SIE8_SELML_88036 are exactly identical! WARNING: Sequences tr_D8RQN2_D8RQN2_SELML_88036 and tr_D8S059_D8S059_SELML_88036 are exactly identical! WARNING: Sequences tr_C0NEI6_C0NEI6_AJECG_447093 and tr_F0UFH2_F0UFH2_AJEC8_544711 are exactly identical! WARNING: Sequences tr_B8P9A6_B8P9A6_POSPM_561896 and tr_A0A1X6NH12_A0A1X6NH12_9APHY_670580 are exactly identical! WARNING: Sequences tr_B8NUN2_B8NUN2_ASPFN_332952 and tr_A0A1S9DHV5_A0A1S9DHV5_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8NUN2_B8NUN2_ASPFN_332952 and tr_A0A2G7GAL4_A0A2G7GAL4_9EURO_656916 are exactly identical! WARNING: Sequences tr_H2Q4E2_H2Q4E2_PANTR_9598 and tr_A0A2R9B4N5_A0A2R9B4N5_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FKB3_F9FKB3_FUSOF_660025 and tr_N4TRT4_N4TRT4_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FKB3_F9FKB3_FUSOF_660025 and tr_X0DY65_X0DY65_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FKB3_F9FKB3_FUSOF_660025 and tr_A0A2H3TD90_A0A2H3TD90_FUSOX_5507 are exactly identical! WARNING: Sequences tr_E9D4X0_E9D4X0_COCPS_443226 and tr_A0A0J7ASU2_A0A0J7ASU2_COCIT_404692 are exactly identical! WARNING: Sequences tr_E9EJ98_E9EJ98_METRA_655844 and tr_A0A0D9P990_A0A0D9P990_METAN_1291518 are exactly identical! WARNING: Sequences tr_A0A158NXY6_A0A158NXY6_ATTCE_12957 and tr_A0A151I3F1_A0A151I3F1_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0E0GLP8_A0A0E0GLP8_ORYNI_4536 and tr_I1PAT9_I1PAT9_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GLP8_A0A0E0GLP8_ORYNI_4536 and tr_A0A0E0NUC1_A0A0E0NUC1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GLP8_A0A0E0GLP8_ORYNI_4536 and tr_A0A0D9Z6J4_A0A0D9Z6J4_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0JBY3_A0A0E0JBY3_ORYNI_4536 and tr_A0A0E0RJI9_A0A0E0RJI9_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0JBY3_A0A0E0JBY3_ORYNI_4536 and tr_A0A0D3HWD5_A0A0D3HWD5_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0JBY3_A0A0E0JBY3_ORYNI_4536 and tr_A0A0E0BUT1_A0A0E0BUT1_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0JBY3_A0A0E0JBY3_ORYNI_4536 and tr_Q2QMP8_Q2QMP8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G7XFR8_G7XFR8_ASPKW_1033177 and tr_A0A146FR79_A0A146FR79_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G2YYS5_G2YYS5_BOTF4_999810 and tr_M7URM8_M7URM8_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SHC1_F2SHC1_TRIRC_559305 and tr_A0A178F011_A0A178F011_TRIRU_5551 are exactly identical! WARNING: Sequences tr_M7ZEJ7_M7ZEJ7_TRIUA_4572 and tr_A0A3B6KAP1_A0A3B6KAP1_WHEAT_4565 are exactly identical! WARNING: Sequences tr_U5GYZ9_U5GYZ9_USTV1_683840 and tr_A0A2X0MBJ9_A0A2X0MBJ9_9BASI_796604 are exactly identical! WARNING: Sequences tr_V2XIS8_V2XIS8_MONRO_1381753 and tr_A0A0W0G488_A0A0W0G488_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A044UC74_A0A044UC74_ONCVO_6282 and tr_A0A182DXK4_A0A182DXK4_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A067GXQ0_A0A067GXQ0_CITSI_2711 and tr_V4T4R2_V4T4R2_9ROSI_85681 are exactly identical! WARNING: Sequences tr_V4U009_V4U009_9ROSI_85681 and tr_A0A2H5PC49_A0A2H5PC49_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0F8U9S5_A0A0F8U9S5_9EURO_308745 and tr_A0A2T5M029_A0A2T5M029_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A091IMD2_A0A091IMD2_EGRGA_188379 and tr_A0A091URG6_A0A091URG6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1S3Y597_A0A1S3Y597_TOBAC_4097 and tr_A0A1U7X1S9_A0A1U7X1S9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3ZST1_A0A1S3ZST1_TOBAC_4097 and tr_A0A1U7VMG9_A0A1U7VMG9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3UY81_A0A1S3UY81_VIGRR_3916 and tr_A0A3Q0FGE6_A0A3Q0FGE6_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A2H3E0E6_A0A2H3E0E6_ARMGA_47427 and tr_A0A2H3C232_A0A2H3C232_9AGAR_1076256 are exactly identical! WARNING: Sequences tr_A0A2H3E0E6_A0A2H3E0E6_ARMGA_47427 and tr_A0A284RAP5_A0A284RAP5_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2D0SSE5_A0A2D0SSE5_ICTPU_7998 and tr_E3TGJ5_E3TGJ5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2G2ZRY5_A0A2G2ZRY5_CAPAN_4072 and tr_A0A2G3CQ43_A0A2G3CQ43_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2G3AER8_A0A2G3AER8_CAPAN_4072 and tr_A0A2G3DBX5_A0A2G3DBX5_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2S7QA66_A0A2S7QA66_9HELO_2070414 and tr_A0A2S7QS57_A0A2S7QS57_9HELO_2070412 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/A6NK58/4_raxmlng_ancestral/A6NK58.raxml.reduced.phy Alignment comprises 1 partitions and 231 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 231 Gaps: 16.26 % Invariant sites: 0.43 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NK58/4_raxmlng_ancestral/A6NK58.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/A6NK58/3_mltree/A6NK58.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 58 / 4640 [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: -135269.395546 [00:00:00 -135269.395546] Initial branch length optimization [00:00:00 -134921.552702] Model parameter optimization (eps = 0.100000) [00:00:20] Tree #1, final logLikelihood: -134566.146888 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.147562,0.272225) (0.221142,0.333955) (0.310396,0.800267) (0.320900,1.986847) 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/A6NK58/4_raxmlng_ancestral/A6NK58.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NK58/4_raxmlng_ancestral/A6NK58.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NK58/4_raxmlng_ancestral/A6NK58.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NK58/4_raxmlng_ancestral/A6NK58.raxml.log Analysis started: 12-Jul-2021 17:25:38 / finished: 12-Jul-2021 17:26:00 Elapsed time: 22.263 seconds Consumed energy: 1.812 Wh